Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/g/gromacs/gromacs_2021.4-2_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/gromacs-2021.4-266d9l7xr/gromacs_2021.4-2_all.buildinfo Get source package info: gromacs=2021.4-2 Source URL: http://snapshot.notset.fr/mr/package/gromacs/2021.4-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 autoconf=2.71-2 automake=1:1.16.5-1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3.1 binutils=2.37-8 binutils-common=2.37-8 binutils-x86-64-linux-gnu=2.37-8 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20211016 chrpath=0.16-2+b1 cmake=3.21.4-1 cmake-data=3.21.4-1 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-10 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-elpa-helper=2.0.9 dh-strip-nondeterminism=1.12.0-2 diffutils=1:3.7-5 distro-info-data=0.52 docutils-common=0.17.1+dfsg-2 doxygen=1.9.1-2 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 emacsen-common=3.0.4 file=1:5.39-3 findutils=4.8.0-1 fontconfig=2.13.1-4.2 fontconfig-config=2.13.1-4.2 fonts-lmodern=2.004.5-6.1 fonts-urw-base35=20200910-1 g++=4:11.2.0-2 g++-11=11.2.0-10 gcc=4:11.2.0-2 gcc-11=11.2.0-10 gcc-11-base=11.2.0-10 gettext=0.21-4 gettext-base=0.21-4 gfortran-11=11.2.0-10 ghostscript=9.54.0~dfsg-5 graphicsmagick=1.4+really1.3.36+hg16481-2 graphviz=2.42.2-5+b1 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 hostname=3.23 ibverbs-providers=36.0-1 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libann0=1.1.2+doc-7 libapache-pom-java=18-1 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2+b1 libasan6=11.2.0-10 libatomic1=11.2.0-10 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1 libavahi-client3=0.8-5 libavahi-common-data=0.8-5 libavahi-common3=0.8-5 libbinutils=2.37-8 libblas-dev=3.10.0-1 libblas3=3.10.0-1 libblkid1=2.37.2-4 libboost-dev=1.74.0.3 libboost1.74-dev=1.74.0-12 libbrotli1=1.0.9-2+b2 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libc-bin=2.32-4 libc-dev-bin=2.32-4 libc6=2.32-4 libc6-dev=2.32-4 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcbor0.8=0.8.0-1 libcc1-0=11.2.0-10 libcdt5=2.42.2-5+b1 libcgraph6=2.42.2-5+b1 libclang-cpp11=1:11.1.0-4 libclang1-11=1:11.1.0-4 libcom-err2=1.46.4-1 libcommons-logging-java=1.2-2 libcommons-parent-java=43-1 libcrypt-dev=1:4.4.25-2 libcrypt1=1:4.4.25-2 libctf-nobfd0=2.37-8 libctf0=2.37-8 libcups2=2.3.3op2-7 libcurl4=7.79.1-1 libdatrie1=0.2.13-2 libdb5.3=5.3.28+dfsg1-0.8 libdbus-1-3=1.12.20-3 libdebconfclient0=0.260 libdebhelper-perl=13.5.2 libdeflate0=1.8-1 libdpkg-perl=1.20.9 libedit2=3.1-20210910-1 libelf1=0.185-2 libevent-2.1-7=2.1.12-stable-1 libevent-core-2.1-7=2.1.12-stable-1 libevent-dev=2.1.12-stable-1 libevent-extra-2.1-7=2.1.12-stable-1 libevent-openssl-2.1-7=2.1.12-stable-1 libevent-pthreads-2.1-7=2.1.12-stable-1 libexpat1=2.4.1-3 libfabric1=1.11.0-2 libffi8=3.4.2-3 libfftw3-bin=3.3.8-2 libfftw3-dev=3.3.8-2 libfftw3-double3=3.3.8-2 libfftw3-long3=3.3.8-2 libfftw3-quad3=3.3.8-2 libfftw3-single3=3.3.8-2 libfido2-1=1.9.0-1 libfile-stripnondeterminism-perl=1.12.0-2 libfontbox-java=1:1.8.16-2 libfontconfig1=2.13.1-4.2 libfontenc1=1:1.1.4-1 libfreetype6=2.11.0+dfsg-1 libfribidi0=1.0.8-2 libgcc-11-dev=11.2.0-10 libgcc-s1=11.2.0-10 libgcrypt20=1.9.4-3+b1 libgd3=2.3.0-2 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgfortran-11-dev=11.2.0-10 libgfortran5=11.2.0-10 libglib2.0-0=2.70.1-1 libgmp10=2:6.2.1+dfsg-2 libgnutls30=3.7.2-2 libgomp1=11.2.0-10 libgpg-error0=1.42-3 libgraphicsmagick-q16-3=1.4+really1.3.36+hg16481-2 libgraphite2-3=1.3.14-1 libgs9=9.54.0~dfsg-5 libgs9-common=9.54.0~dfsg-5 libgssapi-krb5-2=1.18.3-7 libgts-0.7-5=0.7.6+darcs121130-4+b1 libgvc6=2.42.2-5+b1 libgvpr2=2.42.2-5+b1 libharfbuzz0b=2.7.4-1 libhogweed6=3.7.3-1 libhwloc-dev=2.6.0-1 libhwloc-plugins=2.6.0-1 libhwloc15=2.6.0-1 libibverbs-dev=36.0-1 libibverbs1=36.0-1 libice6=2:1.0.10-1 libicu67=67.1-7 libidn12=1.38-4 libidn2-0=2.3.2-2 libijs-0.35=0.35-15 libisl23=0.24-2 libitm1=11.2.0-10 libjbig0=2.1-3.1+b2 libjbig2dec0=0.19-3 libjpeg62-turbo=1:2.0.6-4 libjs-jquery=3.5.1+dfsg+~3.5.5-8 libjs-jquery-ui=1.13.0+dfsg-1 libjs-sphinxdoc=4.2.0-5 libjs-underscore=1.9.1~dfsg-4 libjsoncpp24=1.9.4-5 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkpathsea6=2021.20210626.59705-1 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblab-gamut1=2.42.2-5+b1 liblapack-dev=3.10.0-1 liblapack3=3.10.0-1 liblcms2-2=2.12~rc1-2 libldap-2.4-2=2.4.59+dfsg-1 libllvm11=1:11.1.0-4 liblsan0=11.2.0-10 libltdl-dev=2.4.6-15 libltdl7=2.4.6-15 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmd0=1.0.4-1 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses6=6.2+20210905-1 libncursesw6=6.2+20210905-1 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnl-3-200=3.4.0-1+b1 libnl-3-dev=3.4.0-1+b1 libnl-route-3-200=3.4.0-1+b1 libnl-route-3-dev=3.4.0-1+b1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma-dev=2.0.14-3 libnuma1=2.0.14-3 libopenjp2-7=2.4.0-3 libopenmpi-dev=4.1.2~rc1-5 libopenmpi3=4.1.2~rc1-5 libp11-kit0=0.24.0-5 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpango-1.0-0=1.48.10+ds1-1 libpangocairo-1.0-0=1.48.10+ds1-1 libpangoft2-1.0-0=1.48.10+ds1-1 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpathplan4=2.42.2-5+b1 libpciaccess0=0.16-1 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libpdfbox-java=1:1.8.16-2 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libpixman-1-0=0.40.0-1 libpmix-dev=4.1.1~rc5-1 libpmix2=4.1.1~rc5-1 libpng16-16=1.6.37-3 libprocps8=2:3.3.17-5 libpsl5=0.21.0-1.2 libpsm-infinipath1=3.3+20.604758e7-6.1 libpsm2-2=11.2.185-1 libptexenc1=2021.20210626.59705-1 libpthread-stubs0-dev=0.4-1 libpython3-stdlib=3.9.7-1 libpython3.9-minimal=3.9.8-1 libpython3.9-stdlib=3.9.8-1 libquadmath0=11.2.0-10 librdmacm1=36.0-1 libreadline8=8.1-2 librhash0=1.4.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.3 libsasl2-modules-db=2.1.27+dfsg-2.3 libseccomp2=2.5.2-2 libselinux1=3.1-3+b1 libsemanage-common=3.1-2 libsemanage1=3.1-2 libsepol1=3.1-1 libsigsegv2=2.13-1 libsm6=2:1.2.3-1 libsmartcols1=2.37.2-4 libsqlite3-0=3.36.0-2 libssh2-1=1.10.0-2 libssl1.1=1.1.1l-1 libstdc++-11-dev=11.2.0-10 libstdc++6=11.2.0-10 libsub-override-perl=0.09-2 libsynctex2=2021.20210626.59705-1 libsystemd0=249.5-2 libtasn1-6=4.17.0-2 libteckit0=2.5.10+ds1-3 libtexlua53=2021.20210626.59705-1 libtexluajit2=2021.20210626.59705-1 libthai-data=0.1.28-4.1 libthai0=0.1.28-4.1 libtiff5=4.3.0-2 libtinfo6=6.2+20210905-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-10 libubsan1=11.2.0-10 libuchardet0=0.0.7-1 libucx0=1.11.2-1 libudev1=249.5-2 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libuv1=1.42.0-1 libwebp6=0.6.1-2.1 libwebpmux3=0.6.1-2.1 libwmf0.2-7=0.2.8.4-17+b1 libx11-6=2:1.7.2-2+b1 libx11-data=2:1.7.2-2 libx11-dev=2:1.7.2-2+b1 libxapian30=1.4.18-4 libxau-dev=1:1.0.9-1 libxau6=1:1.0.9-1 libxaw7=2:1.0.13-1.1 libxcb-render0=1.14-3 libxcb-shm0=1.14-3 libxcb1=1.14-3 libxcb1-dev=1.14-3 libxdmcp-dev=1:1.1.2-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxi6=2:1.8-1 libxml2=2.9.12+dfsg-5 libxmu6=2:1.1.2-2+b3 libxnvctrl0=470.82.00-1 libxpm4=1:3.5.12-1 libxrender1=1:0.9.10-1 libxt6=1:1.2.0-1 libz3-4=4.8.12-1+b1 libzstd1=1.4.8+dfsg-3 libzzip-0-13=0.13.72+dfsg.1-1.1 linux-libc-dev=5.14.16-1 login=1:4.8.1-1.1 lsb-base=11.1.0 lsb-release=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 mpi-default-bin=1.14 mpi-default-dev=1.14 mscgen=0.20-14 ncurses-base=6.2+20210905-1 ncurses-bin=6.2+20210905-1 ocl-icd-libopencl1=2.2.14-3 openmpi-bin=4.1.2~rc1-5 openmpi-common=4.1.2~rc1-5 openssh-client=1:8.7p1-1 openssl=1.1.1l-1 passwd=1:4.8.1-1.1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 po-debconf=1.0.21+nmu1 poppler-data=0.4.11-1 preview-latex-style=12.2-1 procps=2:3.3.17-5 python-babel-localedata=2.8.0+dfsg.1-7 python3=3.9.7-1 python3-alabaster=0.7.12-1 python3-babel=2.8.0+dfsg.1-7 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-1 python3-distutils=3.9.7-1 python3-docutils=0.17.1+dfsg-2 python3-idna=2.10-1 python3-imagesize=1.2.0-2 python3-jinja2=3.0.1-2 python3-lib2to3=3.9.7-1 python3-markupsafe=2.0.1-2 python3-minimal=3.9.7-1 python3-packaging=21.0-1 python3-pkg-resources=58.2.0-1 python3-pygments=2.7.1+dfsg-2.1 python3-pyparsing=2.4.7-1 python3-requests=2.25.1+dfsg-2 python3-roman=3.3-1 python3-six=1.16.0-2 python3-snowballstemmer=2.1.0-2 python3-sphinx=4.2.0-5 python3-tz=2021.3-1 python3-urllib3=1.26.5-1~exp1 python3.9=3.9.8-1 python3.9-minimal=3.9.8-1 rdfind=1.5.0-1.1 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sgml-base=1.30 sphinx-common=4.2.0-5 symlinks=1.4-4 sysvinit-utils=3.00-1 t1utils=1.41-4 tar=1.34+dfsg-1 tex-common=6.17 tex-gyre=20180621-3.1 texlive-base=2021.20210921-1 texlive-binaries=2021.20210626.59705-1 texlive-fonts-recommended=2021.20210921-1 texlive-latex-base=2021.20210921-1 texlive-latex-extra=2021.20210921-1 texlive-latex-recommended=2021.20210921-1 texlive-pictures=2021.20210921-1 tzdata=2021e-1 ucf=3.0043 util-linux=2.37.2-4 x11-common=1:7.7+23 x11proto-dev=2021.5-1 xdg-utils=1.1.3-4.1 xfonts-encodings=1:1.0.4-2.1 xfonts-utils=1:7.7+6 xml-core=0.18+nmu1 xorg-sgml-doctools=1:1.11-1.1 xtrans-dev=1.4.0-1 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211111T034125Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211111T034125Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211109T030457Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211108T091209Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d gromacs=2021.4-2 && mkdir -p /build/gromacs-Aby5ZE && dpkg-source --no-check -x /*.dsc /build/gromacs-Aby5ZE/gromacs-2021.4 && chown -R builduser:builduser /build/gromacs-Aby5ZE" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gromacs-Aby5ZE/gromacs-2021.4 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1636423211" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/gromacs-Aby5ZE /tmp/gromacs-2021.4-266d9l7xr bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211108T091209Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.q9_NY8pzZw as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.q9_NY8pzZw Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20211108T091209Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211108T091209Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1035 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4663 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211111T034125Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211111T034125Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211109T030457Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211108T091209Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.q9_NY8pzZw Get:1 http://snapshot.notset.fr/archive/debian/20211111T034125Z bookworm InRelease [128 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211109T030457Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20211108T091209Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20211111T034125Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211111T034125Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211111T034125Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211111T034125Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211111T034125Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211111T034125Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20211111T034125Z bookworm/main Sources [11.7 MB] Get:5 http://snapshot.notset.fr/archive/debian/20211111T034125Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20211109T030457Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20211109T030457Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20211109T030457Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20211109T030457Z unstable/main amd64 Packages [12.0 MB] Fetched 35.1 MB in 29s (1206 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.q9_NY8pzZw I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d gromacs=2021.4-2 && mkdir -p /build/gromacs-Aby5ZE && dpkg-source --no-check -x /*.dsc /build/gromacs-Aby5ZE/gromacs-2021.4 && chown -R builduser:builduser /build/gromacs-Aby5ZE"' exec /tmp/mmdebstrap.q9_NY8pzZw Reading package lists... NOTICE: 'gromacs' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/gromacs.git Please use: git clone https://salsa.debian.org/debichem-team/gromacs.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 86.6 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211111T034125Z bookworm/main gromacs 2021.4-2 (dsc) [2985 B] Get:2 http://snapshot.notset.fr/archive/debian/20211111T034125Z bookworm/main gromacs 2021.4-2 (tar) [48.5 MB] Get:3 http://snapshot.notset.fr/archive/debian/20211111T034125Z bookworm/main gromacs 2021.4-2 (tar) [38.0 MB] Get:4 http://snapshot.notset.fr/archive/debian/20211111T034125Z bookworm/main gromacs 2021.4-2 (diff) [40.9 kB] Fetched 86.6 MB in 1min 8s (1279 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'gromacs_2021.4-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting gromacs in /build/gromacs-Aby5ZE/gromacs-2021.4 dpkg-source: info: unpacking gromacs_2021.4.orig.tar.gz dpkg-source: info: unpacking gromacs_2021.4.orig-regressiontests.tar.gz dpkg-source: info: unpacking gromacs_2021.4-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying readme.patch dpkg-source: info: applying copyright-file.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying local-mathjax.patch dpkg-source: info: applying mpi-tests-localhost.patch dpkg-source: info: applying i386-disable-specific-tests.patch dpkg-source: info: applying hppa-disable-ewaldunittest.patch dpkg-source: info: applying manual-image-conversion.patch dpkg-source: info: applying gammadistribution-test.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gromacs-Aby5ZE/gromacs-2021.4 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1636423211" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.q9_NY8pzZw dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2021.4-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nicholas Breen dpkg-source --before-build . debian/rules clean dh_testdir dh_testroot rm -rf build docs/doxygen/*.pyc dh_clean build-basic build-mpi build-manual configure-stamp debian/rules binary-indep dh_testdir (mkdir -p build/basic; cd build/basic; cmake \ /build/gromacs-Aby5ZE/gromacs-2021.4 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2021.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=OFF -DGMX_X11=ON -DGMX_INSTALL_LEGACY_API=ON ) -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.8", minimum required is "3.6") found components: Interpreter -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Using default binary suffix: "" -- Using default library suffix: "" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5") -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz -- Detected build CPU family - 6 -- Detected build CPU model - 79 -- Detected build CPU stepping - 1 -- Detected build CPU features - aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "4.2.0", minimum required is "1.6.1") found components: pygments -- Check if compiler accepts -pthread -- Check if compiler accepts -pthread - yes -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake \ /build/gromacs-Aby5ZE/gromacs-2021.4 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2021.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=OFF -DGMX_X11=ON -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.8", minimum required is "3.6") found components: Interpreter -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5") -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz -- Detected build CPU family - 6 -- Detected build CPU model - 79 -- Detected build CPU stepping - 1 -- Detected build CPU features - aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3, trying generic detection -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "4.2.0", minimum required is "1.6.1") found components: pygments -- Check if compiler accepts -pthread -- Check if compiler accepts -pthread - yes -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp (mkdir -p build/mpi; cd build/mpi; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/gromacs-Aby5ZE/gromacs-2021.4 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2021.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi" -DGMX_LIBS_SUFFIX="_mpi") -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.8", minimum required is "3.6") found components: Interpreter -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- Using manually set binary suffix: "_mpi" -- Using manually set library suffix: "_mpi" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz -- Detected build CPU family - 6 -- Detected build CPU model - 79 -- Detected build CPU stepping - 1 -- Detected build CPU features - aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- The mdrun-only build is deprecated -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi (mkdir -p build/mpi-dp; cd build/mpi-dp; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/gromacs-Aby5ZE/gromacs-2021.4 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2021.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d" -DGMX_LIBS_SUFFIX="_mpi_d") -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.8", minimum required is "3.6") found components: Interpreter -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- Using manually set binary suffix: "_mpi_d" -- Using manually set library suffix: "_mpi_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz -- Detected build CPU family - 6 -- Detected build CPU model - 79 -- Detected build CPU stepping - 1 -- Detected build CPU features - aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3, trying generic detection -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- The mdrun-only build is deprecated -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp touch configure-stamp dh_testdir /usr/bin/make -j10 -C build/basic make[1]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' /usr/bin/cmake -S/build/gromacs-Aby5ZE/gromacs-2021.4 -B/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/CMakeFiles /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/selection /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/selection /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs 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src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/errhandler.cpp /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/linearalgebra /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= /usr/bin/make -f 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/usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/tmpi_malloc.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' /usr/bin/make -f 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/lock.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/mdrun/mdrun.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/system_error.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/legacymodules.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/coder.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/alltoall.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF 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CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/constraintelement.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/barrier.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/p2p_send_recv.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/bcast.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/dict.c make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/p2p_wait.cpp [ 0%] Built target gmx_objlib /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/fixpoint.c make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/3dview.cpp.o -MF CMakeFiles/view_objlib.dir/view/3dview.cpp.o.d -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/3dview.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/huffman.c make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' [ 0%] Built target lmfit_objlib cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/collective.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/rle.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem 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-ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/profile.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/energydata.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers 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-DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/filter.cpp.o -MF CMakeFiles/view_objlib.dir/view/filter.cpp.o.d -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/filter.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/warnmalloc.c make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' [ 0%] Built target mdrun_objlib cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/molps.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' [ 1%] Built target linearalgebra cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/scan.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/numa_malloc.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd 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/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/selection/scanner.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/nleg.cpp.o -MF CMakeFiles/view_objlib.dir/view/nleg.cpp.o.d -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/nleg.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/pulldown.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' [ 1%] Built target scanner cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o -MF CMakeFiles/view_objlib.dir/view/view.cpp.o.d -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/view.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlg.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/xdlg.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o -MF CMakeFiles/modularsimulator.dir/propagator.cpp.o.d -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/propagator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/xdlghi.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/xdlgitem.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/lib/md5.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/statepropagatordata.cpp cd 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/once.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/trajectoryelement.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' [ 5%] Built target thread_mpi cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' [ 7%] Built target view_objlib make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' [ 9%] Built target tng_io_obj make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' [ 11%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/gromacs-Aby5ZE/gromacs-2021.4/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/alignedallocator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/any.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/basenetwork.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/baseversion.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/binaryinformation.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/compare.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/coolstuff.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/cstringutil.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/datafilefinder.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/directoryenumerator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/errorcodes.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/errorformat.cpp In file included from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/binaryinformation.cpp:77: /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/buildinfo.h:75: warning: "HWLOC_VERSION" redefined 75 | #define HWLOC_VERSION "2.5.0" | In file included from /usr/include/hwloc.h:56, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/binaryinformation.cpp:64: /usr/include/x86_64-linux-gnu/hwloc/autogen/config.h:15: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.6.0" | cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c 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-O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/fileredirector.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/filestream.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/futil.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/gmxassert.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/gmxomp.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/init.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/inmemoryserializer.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/readrot.cpp In file included from /usr/include/c++/11/string:40, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/streambuf:41, from /usr/include/c++/11/bits/streambuf_iterator.h:35, from /usr/include/c++/11/iterator:66, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/arrayref.h:54, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/h_db.h:45, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/h_db.cpp:41: In static member function ‘static constexpr std::size_t std::char_traits::length(const char_type*)’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::assign(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/11/bits/basic_string.h:1458:19, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/11/bits/basic_string.h:689:28, inlined from ‘void read_ab(char*, const char*, MoleculePatch*)’ at /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/h_db.cpp:115:25: /usr/include/c++/11/bits/char_traits.h:371:32: warning: ‘long unsigned int __builtin_strlen(const char*)’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread] 371 | return __builtin_strlen(__s); | ~~~~~~~~~~~~~~~~^~~~~ /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/h_db.cpp: In function ‘void read_ab(char*, const char*, MoleculePatch*)’: /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/h_db.cpp:88:10: note: at offset 48 into source object ‘a’ of size 48 88 | char a[4][12]; | ^ cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. 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/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/solvate.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/specbond.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o selection/CMakeFiles/scanner.dir/parser.cpp.o selection/CMakeFiles/scanner.dir/scanner.cpp.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so -lpthread -lm /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblapack.so -lpthread -lm /usr/lib/gcc/x86_64-linux-gnu/11/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.6.0.0 ../../lib/libgromacs.so.6 ../../lib/libgromacs.so make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' [ 96%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/share/template /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/share/template /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic 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-Wl,-z,relro -Wl,-z,now CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx ../../lib/libgromacs.so.6.0.0 /usr/lib/x86_64-linux-gnu/libX11.so -lm /usr/lib/gcc/x86_64-linux-gnu/11/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/gmxcalculator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 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CMakeFiles/nblib.dir/interactions.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/interactions.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/molecules.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/particlesequencer.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' [ 98%] Built target gmx cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api 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-ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/simulationstate.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/topologyhelpers.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/util/setup.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib.so.0 -o ../../lib/libnblib.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/forcecalculator.cpp.o CMakeFiles/nblib.dir/gmxcalculator.cpp.o CMakeFiles/nblib.dir/gmxsetup.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o ../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/11/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib.so.0.1.0 ../../lib/libnblib.so.0 ../../lib/libnblib.so make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend /usr/bin/make -f 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'/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' /usr/bin/cmake -E cmake_progress_start /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic/CMakeFiles 0 make[1]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic' /usr/bin/make -j10 -C build/basic-dp make[1]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' /usr/bin/cmake -S/build/gromacs-Aby5ZE/gromacs-2021.4 -B/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/CMakeFiles /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make 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'/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/mdrun/mdrun.cpp make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3.9 -D PROJECT_VERSION=2021.4-Debian-2021.4-2 -D PROJECT_SOURCE_DIR=/build/gromacs-Aby5ZE/gromacs-2021.4 -D VERSION_CMAKEIN=/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2021.4-2 -P /build/gromacs-Aby5ZE/gromacs-2021.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 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src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/legacymodules.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -MF CMakeFiles/view_objlib.dir/view/dialogs.cpp.o.d -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/dialogs.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/bwt.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/system_error.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/coder.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/dict.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/alltoall.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/selection/scanner.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/p2p_protocol.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/huffman.c make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/barrier.cpp [ 0%] Built target gmx_objlib cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/p2p_send_recv.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/bcast.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/mdrun/nonbonded_bench.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/p2p_wait.cpp [ 0%] Built target lmfit_objlib cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/collective.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/profile.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -MF CMakeFiles/view_objlib.dir/view/fgrid.cpp.o.d -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/fgrid.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/filter.cpp.o -MF CMakeFiles/view_objlib.dir/view/filter.cpp.o.d -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/filter.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/comm.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/reduce.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/event.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/reduce_fast.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/gather.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem 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src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT 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src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/nmol.cpp.o -MF CMakeFiles/view_objlib.dir/view/nmol.cpp.o.d -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/nmol.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' [ 0%] Built target mdrun_objlib cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/popup.cpp.o -MF CMakeFiles/view_objlib.dir/view/popup.cpp.o.d -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/popup.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/lib/md5.c make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' [ 0%] Built target scanner cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra/matrix.cpp cd 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-DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -MF CMakeFiles/view_objlib.dir/view/pulldown.cpp.o.d -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/pulldown.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat 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CMakeFiles/view_objlib.dir/view/x11.cpp.o.d -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/x11.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlg.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/xdlg.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/xdlghi.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/xdlgitem.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xmb.cpp.o -MF CMakeFiles/view_objlib.dir/view/xmb.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/xmb.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' [ 1%] Built target linearalgebra cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/constraintelement.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' [ 5%] Built target thread_mpi cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/domdechelper.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xutil.cpp.o -MF CMakeFiles/view_objlib.dir/view/xutil.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/view/xutil.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/energydata.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o -MF CMakeFiles/modularsimulator.dir/forceelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/forceelement.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' [ 7%] Built target view_objlib cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o -MF CMakeFiles/modularsimulator.dir/propagator.cpp.o.d -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/propagator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/topologyholder.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' [ 9%] Built target tng_io_obj make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' [ 11%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/gromacs-Aby5ZE/gromacs-2021.4/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/alignedallocator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/any.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/basenetwork.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/baseversion.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/binaryinformation.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/compare.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/coolstuff.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/cstringutil.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/datafilefinder.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/directoryenumerator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/errorcodes.cpp In file included from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/binaryinformation.cpp:77: /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/buildinfo.h:75: warning: "HWLOC_VERSION" redefined 75 | #define HWLOC_VERSION "2.5.0" | In file included from /usr/include/hwloc.h:56, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/binaryinformation.cpp:64: /usr/include/x86_64-linux-gnu/hwloc/autogen/config.h:15: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.6.0" | cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/errorformat.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/exceptions.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/fatalerror.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/fileredirector.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/init.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/pdb2top.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/pgutil.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/readir.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/readpull.cpp In file included from /usr/include/c++/11/string:40, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/streambuf:41, from /usr/include/c++/11/bits/streambuf_iterator.h:35, from /usr/include/c++/11/iterator:66, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/arrayref.h:54, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/h_db.h:45, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/h_db.cpp:41: In static member function ‘static constexpr std::size_t std::char_traits::length(const char_type*)’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::assign(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/11/bits/basic_string.h:1458:19, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/11/bits/basic_string.h:689:28, inlined from ‘void read_ab(char*, const char*, MoleculePatch*)’ at /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/h_db.cpp:115:25: /usr/include/c++/11/bits/char_traits.h:371:32: warning: ‘long unsigned int __builtin_strlen(const char*)’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread] 371 | return __builtin_strlen(__s); | ~~~~~~~~~~~~~~~~^~~~~ /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/h_db.cpp: In function ‘void read_ab(char*, const char*, MoleculePatch*)’: /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/h_db.cpp:88:10: note: at offset 48 into source object ‘a’ of size 48 88 | char a[4][12]; | ^ cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/readrot.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/resall.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxpreprocess/solvate.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/usr/lib/x86_64-linux-gnu/libblas.so -lpthread -lm /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblapack.so -lpthread -lm /usr/lib/gcc/x86_64-linux-gnu/11/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.6.0.0 ../../lib/libgromacs_d.so.6 ../../lib/libgromacs_d.so make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' [ 96%] Built target libgromacs /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 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'/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers 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/build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/forcecalculator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/gmxcalculator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxsetup.cpp.o -MF CMakeFiles/nblib.dir/gmxsetup.cpp.o.d -o CMakeFiles/nblib.dir/gmxsetup.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/gmxsetup.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/integrator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/interactions.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/molecules.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/particlesequencer.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/particletype.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.6.0.0 /usr/lib/x86_64-linux-gnu/libX11.so -lm /usr/lib/gcc/x86_64-linux-gnu/11/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' [ 98%] Built target gmx cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/simulationstate.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/topologyhelpers.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/topology.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/listed_forces/calculator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/listed_forces/transformations.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/api -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/api/nblib/util/setup.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib.so.0 -o ../../lib/libnblib.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/forcecalculator.cpp.o CMakeFiles/nblib.dir/gmxcalculator.cpp.o CMakeFiles/nblib.dir/gmxsetup.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o ../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/11/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib.so.0.1.0 ../../lib/libnblib.so.0 ../../lib/libnblib.so make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make 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../../../bin/argon-forces-integration ../../../lib/libnblib.so.0.1.0 -Wl,-rpath-link,/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/lib make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' [100%] Built target argon-forces-integration cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -o ../../../bin/methane-water-integration ../../../lib/libnblib.so.0.1.0 -Wl,-rpath-link,/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/lib make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp/CMakeFiles 0 make[1]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/basic-dp' touch build-basic dh_testdir /usr/bin/make -j10 -C build/mpi make[1]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' /usr/bin/cmake -S/build/gromacs-Aby5ZE/gromacs-2021.4 -B/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/CMakeFiles /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/linearalgebra /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/modularsimulator /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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VERSION_OUT=/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2021.4-2 -P /build/gromacs-Aby5ZE/gromacs-2021.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++17 -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit/lmmin.cpp make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/bwlzh.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/bwt.c make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/checkpointhelper.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/mdrun/mdrun.cpp make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra/eigensolver.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' [ 0%] Built target release-version-info cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/mdrun/nonbonded_bench.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/atomic.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/coder.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/system_error.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/dict.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/huffman.c make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' [ 1%] Built target thread_mpi cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o -MF CMakeFiles/linearalgebra.dir/nrjac.cpp.o.d -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/mtf.c make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' [ 1%] Built target mdrun_objlib cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/rle.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/tng_compress.c make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' [ 1%] Built target lmfit_objlib cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/constraintelement.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/vals16.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o 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CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/domdechelper.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/energydata.cpp cd 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/lib/md5.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' [ 1%] Built target scanner cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/signallers.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' [ 2%] Built target linearalgebra cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF 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/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' [ 5%] Built target tng_io_obj make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/gromacs-Aby5ZE/gromacs-2021.4/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/alignedallocator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/basenetwork.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/baseversion.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/binaryinformation.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/compare.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/coolstuff.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/cstringutil.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/datafilefinder.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/directoryenumerator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/errorcodes.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/errorformat.cpp In file included from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/binaryinformation.cpp:77: /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/buildinfo.h:75: warning: "HWLOC_VERSION" redefined 75 | #define HWLOC_VERSION "2.5.0" | In file included from /usr/include/hwloc.h:56, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/binaryinformation.cpp:64: /usr/include/x86_64-linux-gnu/hwloc/autogen/config.h:15: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.6.0" | cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/fileredirector.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o 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/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include 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/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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&& /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 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-DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 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&& /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o 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/usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o 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make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/selection/parser.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3.9 -D PROJECT_VERSION=2021.4-Debian-2021.4-2 -D PROJECT_SOURCE_DIR=/build/gromacs-Aby5ZE/gromacs-2021.4 -D VERSION_CMAKEIN=/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2021.4-2 -P /build/gromacs-Aby5ZE/gromacs-2021.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/selection/scanner.cpp make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++17 -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit/lmmin.cpp make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/errhandler.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/tmpi_malloc.cpp make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra/eigensolver.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/bwlzh.c make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/checkpointhelper.cpp make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/mdrun/mdrun.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' [ 0%] Built target release-version-info cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops 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src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/atomic.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o -MF CMakeFiles/linearalgebra.dir/nrjac.cpp.o.d -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra/nrjac.cpp cd 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/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/bwt.c make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' [ 1%] Built target thread_mpi cd 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/rle.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/vals16.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/warnmalloc.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/xtc2.c make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' [ 1%] Built target lmfit_objlib cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/lib/md5.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/constraintelement.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/domdechelper.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/energydata.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o -MF CMakeFiles/modularsimulator.dir/forceelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/forceelement.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' [ 1%] Built target mdrun_objlib cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' [ 1%] Built target scanner cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o -MF CMakeFiles/modularsimulator.dir/propagator.cpp.o.d -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/propagator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o -MF CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/signallers.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' [ 2%] Built target linearalgebra cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/topologyholder.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' [ 5%] Built target tng_io_obj make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/gromacs-Aby5ZE/gromacs-2021.4/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 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-ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/any.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/basenetwork.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/binaryinformation.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/compare.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/coolstuff.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/datafilefinder.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/directoryenumerator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem 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-DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/errorformat.cpp In file included from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/binaryinformation.cpp:77: /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/buildinfo.h:75: warning: "HWLOC_VERSION" redefined 75 | #define HWLOC_VERSION "2.5.0" | In file included from /usr/include/hwloc.h:56, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/binaryinformation.cpp:64: /usr/include/x86_64-linux-gnu/hwloc/autogen/config.h:15: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.6.0" | cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/fileredirector.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c 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/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF 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-DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/mpi-dp/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF 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not found -- Using default binary suffix: "" -- Using default library suffix: "" -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz -- Detected build CPU family - 6 -- Detected build CPU model - 79 -- Detected build CPU stepping - 1 -- Detected build CPU features - aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "4.2.0", minimum required is "1.6.1") found components: pygments -- Found LATEX: /usr/bin/latex -- Check if compiler accepts -pthread -- Check if compiler accepts -pthread - yes -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation /usr/bin/make -j10 gmx -C build/documentation make[1]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' /usr/bin/cmake -S/build/gromacs-Aby5ZE/gromacs-2021.4 -B/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 gmx make[2]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' /usr/bin/cmake -S/build/gromacs-Aby5ZE/gromacs-2021.4 -B/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/CMakeFiles 47 /usr/bin/make -f CMakeFiles/Makefile2 src/programs/CMakeFiles/gmx.dir/all make[3]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 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src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/linearalgebra /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/selection/parser.cpp make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/gmx.cpp make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/adler32.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/adler32.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/adler32.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib/adler32.c /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3.9 -D PROJECT_VERSION=2021.4-Debian-2021.4-2 -D PROJECT_SOURCE_DIR=/build/gromacs-Aby5ZE/gromacs-2021.4 -D VERSION_CMAKEIN=/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2021.4-2 -P /build/gromacs-Aby5ZE/gromacs-2021.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/errhandler.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/mdrun/mdrun.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/checkpointhelper.cpp make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' [ 0%] Built target release-version-info cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem 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/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/trees.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/trees.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/trees.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib/trees.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/dict.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs/legacymodules.cpp make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/system_error.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/huffman.c [ 0%] Built target lmfit_objlib cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/alltoall.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/p2p_protocol.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/uncompr.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/uncompr.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/uncompr.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib/uncompr.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib/zutil.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/barrier.cpp make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' [ 2%] Built target tng_io_zlib /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/reduce.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/event.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/selection/scanner.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/reduce_fast.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/gather.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/scatter.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o -MF CMakeFiles/linearalgebra.dir/nrjac.cpp.o.d -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/group.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/tmpi_init.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -I/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/external/zlib -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/src/lib/md5.c cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/topology.cpp make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/compositesimulatorelement.cpp [ 2%] Built target view_objlib cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/list.cpp make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' [ 2%] Built target linearalgebra cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/constraintelement.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/domdechelper.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/energydata.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/type.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o -MF CMakeFiles/modularsimulator.dir/forceelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/forceelement.cpp make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' [ 2%] Built target scanner cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' [ 2%] Built target mdrun_objlib cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/scan.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/numa_malloc.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/src/once.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' [ 4%] Built target thread_mpi cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o -MF CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/signallers.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/topologyholder.cpp make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' [ 6%] Built target tng_io_obj cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/gromacs-Aby5ZE/gromacs-2021.4/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/utility/alignedallocator.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem 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/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF 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-DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o 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-I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c 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/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_analyze.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_angle.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_awh.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_bar.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_bundle.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_chi.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_cluster.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_confrms.cpp /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_anaeig.cpp: In function ‘void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)’: /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_anaeig.cpp:814:24: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 4094 [-Wformat-overflow=] 814 | sprintf(c, "%%d%s", str2); /* append '%s' and extention to filename */ | ^~ ~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6606, from /usr/include/c++/11/string:55, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_anaeig.cpp:46: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 3 and 4098 bytes into a destination of size 4096 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_anaeig.cpp:814:24: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 4094 [-Wformat-overflow=] 814 | sprintf(c, "%%d%s", str2); /* append '%s' and extention to filename */ | ^~ ~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6606, from /usr/include/c++/11/string:55, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_anaeig.cpp:46: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 3 and 4098 bytes into a destination of size 4096 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_anaeig.cpp:814:24: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 4094 [-Wformat-overflow=] 814 | sprintf(c, "%%d%s", str2); /* append '%s' and extention to filename */ | ^~ ~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6606, from /usr/include/c++/11/string:55, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/gmxana/gmx_anaeig.cpp:46: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 3 and 4098 bytes into a destination of size 4096 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem 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/build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/fileio/warninp.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/fileio/writeps.cpp /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/fileio/checkpoint.cpp: In function ‘int doVectorLow(XDR*, StatePart, int, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator]’: /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/fileio/checkpoint.cpp:795:31: warning: ‘this’ pointer is null [-Wnonnull] 795 | vector->resize(numElemInTheFile); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/fileio/checkpoint.h:44, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/fileio/checkpoint.cpp:42: /usr/include/c++/11/bits/stl_vector.h:937:7: note: in a call to non-static member function ‘void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type) [with _Tp = int; _Alloc = std::allocator]’ 937 | resize(size_type __new_size) | ^~~~~~ cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/fileio/xdrd.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/fileio/xtcio.cpp /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/fileio/checkpoint.cpp: In function ‘int doVectorLow(XDR*, StatePart, int, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = gmx::Allocator]’: /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/fileio/checkpoint.cpp:795:31: warning: ‘this’ pointer is null [-Wnonnull] 795 | vector->resize(numElemInTheFile); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/fileio/checkpoint.h:44, from /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/fileio/checkpoint.cpp:42: /usr/include/c++/11/bits/stl_vector.h:937:7: note: in a call to non-static member function ‘void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type) [with _Tp = float; _Alloc = gmx::Allocator]’ 937 | resize(size_type __new_size) | ^~~~~~ cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/fileio/xvgr.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/selection/centerofmass.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/selection/compiler.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/selection/evaluate.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/selection/indexutil.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/selection/mempool.cpp cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src -I/build/gromacs-Aby5ZE/gromacs-2021.4/src -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/thread_mpi/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/tng_io/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/tng/include -isystem /build/gromacs-Aby5ZE/gromacs-2021.4/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-Aby5ZE/gromacs-2021.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/selection/nbsearch.cpp cd 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/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs/modularsimulator /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/programs 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src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build Consolidate compiler generated dependencies of target tng_io_zlib Consolidate compiler generated dependencies of target tng_io_obj make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' Consolidate compiler generated dependencies of target mdrun_objlib Consolidate compiler generated dependencies of target linearalgebra Consolidate compiler generated dependencies of target scanner make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build /usr/bin/make -f 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Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/reference-manual/analysis/plots/sgangle.pdf /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/sgangle.pdf cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-Aby5ZE/gromacs-2021.4/docs/conf.cmakein.py -D VERSION_OUT=/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/conf.py -D CMAKE_MINIMUM_REQUIRED_VERSION=3.13 -D EXPECTED_DOXYGEN_VERSION=1.8.5 -D EXPECTED_SPHINX_VERSION=1.6.1 -D GMX_ADMIN_DIR=/build/gromacs-Aby5ZE/gromacs-2021.4/admin -D GMX_LMFIT_REQUIRED_VERSION=7.0 -D "GMX_MANUAL_DOI_STRING=This is not a release build of GROMACS, so please reference one of the GROMACS papers and the base release of the manual." -D GMX_TNG_MINIMUM_REQUIRED_VERSION=1.7.10 -D "GMX_SOURCE_DOI_STRING=This is not a release build of GROMACS. Please reference one of the GROMACS papers, as well as the base release that this version is built from. Also, please state what modifcations have been performed or where the version was sourced from." -D GMXAPI_PYTHON_STAGING_DIR= -D IMAGE_CONVERT_STRING=possible -D REGRESSIONTEST_VERSION=2021.4 -D REQUIRED_CUDA_COMPUTE_CAPABILITY= -D REQUIRED_CUDA_VERSION= -D REQUIRED_OPENCL_MIN_VERSION= -D REGRESSIONTEST_MD5SUM_STRING=unknown -D RELENG_PATH= -D SOURCE_MD5SUM=unknown -D SPHINX_EXTENSION_PATH=/build/gromacs-Aby5ZE/gromacs-2021.4/docs -P /build/gromacs-Aby5ZE/gromacs-2021.4/cmake/gmxConfigureVersionInfo.cmake make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/gromacs /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/gromacs 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cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/gm convert /build/gromacs-Aby5ZE/gromacs-2021.4/docs/reference-manual/algorithms/plots/flowchart.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/flowchart.png cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/gm convert /build/gromacs-Aby5ZE/gromacs-2021.4/docs/reference-manual/algorithms/plots/free1.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/free1.png cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/dev-manual/containers.rst /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/dev-manual/containers.rst 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copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/dev-manual/doxygen.rst /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/dev-manual/doxygen.rst cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/gm convert /build/gromacs-Aby5ZE/gromacs-2021.4/docs/reference-manual/algorithms/plots/leapfrog.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/leapfrog.png cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/gm convert /build/gromacs-Aby5ZE/gromacs-2021.4/docs/reference-manual/algorithms/plots/lincs.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/lincs.png cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy 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convert /build/gromacs-Aby5ZE/gromacs-2021.4/docs/reference-manual/special/plots/dumaro.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input//reference-manual/special/plots/dumaro.png cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/release-notes/2019/2019.1.rst /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/release-notes/2019/2019.1.rst cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/gm convert /build/gromacs-Aby5ZE/gromacs-2021.4/docs/reference-manual/special/plots/dumtypes.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input//reference-manual/special/plots/dumtypes.png cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/release-notes/2019/major/highlights.rst /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/release-notes/2019/major/highlights.rst cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/release-notes/2019/major/features.rst /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/release-notes/2019/major/features.rst cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/release-notes/2019/major/performance.rst /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/release-notes/2019/major/performance.rst cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/gm convert /build/gromacs-Aby5ZE/gromacs-2021.4/docs/reference-manual/special/plots/equipotential.pdf -antialias -quality 03 -pointsize 12 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make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/gm convert /build/gromacs-Aby5ZE/gromacs-2021.4/docs/reference-manual/special/plots/rotation.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input//reference-manual/special/plots/rotation.png cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/release-notes/2016/2016.1.rst /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/release-notes/2016/2016.1.rst cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/release-notes/2016/major/highlights.rst /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/release-notes/2016/major/highlights.rst cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/release-notes/2016/major/new-features.rst /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/release-notes/2016/major/new-features.rst cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/gm convert /build/gromacs-Aby5ZE/gromacs-2021.4/docs/reference-manual/analysis/plots/dih-def.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/dih-def.png [ 70%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-Aby5ZE/gromacs-2021.4 /build/gromacs-Aby5ZE/gromacs-2021.4/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/programs /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/release-notes/2016/major/performance.rst /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/release-notes/2016/major/performance.rst make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/release-notes/2016/major/tools.rst /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/release-notes/2016/major/tools.rst cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/release-notes/2016/major/bugs-fixed.rst /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/release-notes/2016/major/bugs-fixed.rst make[4]: Entering directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation' cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/release-notes/2016/major/removed-features.rst 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/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/user-guide/mdrun-features.rst cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/user-guide/mdrun-performance.rst /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/user-guide/mdrun-performance.rst cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/gm convert /build/gromacs-Aby5ZE/gromacs-2021.4/docs/reference-manual/analysis/plots/hbond-insert.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/hbond-insert.png cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/user-guide/run-time-errors.rst 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/build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/nblib/guide-to-writing-MD-programs.rst cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/reference-manual/index.rst /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/reference-manual/index.rst cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-Aby5ZE/gromacs-2021.4/docs/reference-manual/preface.rst /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs/sphinx-input/reference-manual/preface.rst cd /build/gromacs-Aby5ZE/gromacs-2021.4/build/documentation/docs && /usr/bin/gm convert /build/gromacs-Aby5ZE/gromacs-2021.4/docs/reference-manual/analysis/plots/hbond.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch 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