Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/a/apbs/apbs_3.4.1-2_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/apbs-3.4.1-2clh41mvc/apbs_3.4.1-2_all.buildinfo Get source package info: apbs=3.4.1-2 Source URL: http://snapshot.notset.fr/mr/package/apbs/3.4.1-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.121 autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6.1 binutils=2.38-4 binutils-common=2.38-4 binutils-x86-64-linux-gnu=2.38-4 bsdextrautils=2.38-4 bsdutils=1:2.38-4 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 cmake=3.23.2-1 cmake-data=3.23.2-1 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.3.0-3 cpp-12=12.1.0-2 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.7.1 debianutils=5.7-0.2 dh-autoreconf=20 dh-elpa-helper=2.0.10 dh-python=5.20220403 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 docutils-common=0.17.1+dfsg-2 dpkg=1.21.8 dpkg-dev=1.21.8 dwz=0.14-1 emacsen-common=3.0.4 file=1:5.41-4 findutils=4.9.0-3 fonts-font-awesome=5.0.10+really4.7.0~dfsg-4.1 fonts-lato=2.0-2.1 fonts-mathjax=2.7.9+dfsg-1 g++=4:11.2.0-2 g++-11=11.3.0-3 gcc=4:11.2.0-2 gcc-11=11.3.0-3 gcc-11-base=11.3.0-3 gcc-12=12.1.0-2 gcc-12-base=12.1.0-2 gettext=0.21-6 gettext-base=0.21-6 gfortran-12=12.1.0-2 grep=3.7-1 groff-base=1.22.4-8 gzip=1.12-1 hostname=3.23 ibverbs-providers=40.0-1 init-system-helpers=1.63 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libamd2=1:5.12.0+dfsg-1 libarchive-zip-perl=1.68-1 libarchive13=3.6.0-1 libarpack2=3.8.0-1 libarpack2-dev=3.8.0-1 libasan6=11.3.0-3 libasan8=12.1.0-2 libatomic1=12.1.0-2 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbinutils=2.38-4 libblas-dev=3.10.1-2 libblas3=3.10.1-2 libblkid1=2.38-4 libbrotli1=1.0.9-2+b3 libbsd0=0.11.6-1 libbtf1=1:5.12.0+dfsg-1 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcamd2=1:5.12.0+dfsg-1 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcbor0.8=0.8.0-2 libcc1-0=12.1.0-2 libccolamd2=1:5.12.0+dfsg-1 libcholmod3=1:5.12.0+dfsg-1 libcolamd2=1:5.12.0+dfsg-1 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-4 libctf0=2.38-4 libcurl3-gnutls=7.83.1-1+b1 libcurl4=7.83.1-1+b1 libcxsparse3=1:5.12.0+dfsg-1 libdb5.3=5.3.28+dfsg1-0.9 libdebconfclient0=0.262 libdebhelper-perl=13.7.1 libdpkg-perl=1.21.8 libedit2=3.1-20210910-1 libelf1=0.187-1 libevent-2.1-7=2.1.12-stable-5+b1 libevent-core-2.1-7=2.1.12-stable-5+b1 libevent-dev=2.1.12-stable-5+b1 libevent-extra-2.1-7=2.1.12-stable-5+b1 libevent-openssl-2.1-7=2.1.12-stable-5+b1 libevent-pthreads-2.1-7=2.1.12-stable-5+b1 libexpat1=2.4.8-1 libexpat1-dev=2.4.8-1 libfabric1=1.11.0-3 libffi8=3.4.2-4 libfido2-1=1.11.0-1+b1 libfile-stripnondeterminism-perl=1.13.0-1 libgcc-11-dev=11.3.0-3 libgcc-12-dev=12.1.0-2 libgcc-s1=12.1.0-2 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgfortran-12-dev=12.1.0-2 libgfortran5=12.1.0-2 libglib2.0-0=2.72.1-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.4-2 libgomp1=12.1.0-2 libgpg-error0=1.45-2 libgssapi-krb5-2=1.19.2-2+b2 libhogweed6=3.7.3-1 libhwloc-dev=2.7.1-1 libhwloc-plugins=2.7.1-1 libhwloc15=2.7.1-1 libibverbs-dev=40.0-1 libibverbs1=40.0-1 libicu71=71.1-3 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=12.1.0-2 libjs-jquery=3.6.0+dfsg+~3.5.13-1 libjs-jquery-ui=1.13.1+dfsg-1 libjs-mathjax=2.7.9+dfsg-1 libjs-sphinxdoc=4.5.0-3 libjs-underscore=1.13.3~dfsg+~1.11.4-1 libjsoncpp25=1.9.5-4 libk5crypto3=1.19.2-2+b2 libkeyutils1=1.6.1-3 libklu1=1:5.12.0+dfsg-1 libkrb5-3=1.19.2-2+b2 libkrb5support0=1.19.2-2+b2 liblapack-dev=3.10.1-2 liblapack3=3.10.1-2 libldap-2.5-0=2.5.12+dfsg-2 libldl2=1:5.12.0+dfsg-1 liblsan0=12.1.0-2 libltdl-dev=2.4.7-4 libltdl7=2.4.7-4 liblz4-1=1.9.3-2 liblzma5=5.2.5-2.1 libmagic-mgc=1:5.41-4 libmagic1=1:5.41-4 libmaloc-dev=1.5-1 libmaloc1=1.5-1 libmd0=1.0.4-1 libmetis5=5.1.0.dfsg-7 libmongoose2=1:5.12.0+dfsg-1 libmount1=2.38-4 libmpc3=1.2.1-2 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses6=6.3+20220423-2 libncursesw6=6.3+20220423-2 libnettle8=3.7.3-1 libnghttp2-14=1.47.0-1+b1 libnl-3-200=3.5.0-0.1 libnl-3-dev=3.5.0-0.1 libnl-route-3-200=3.5.0-0.1 libnl-route-3-dev=3.5.0-0.1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma-dev=2.0.14-3 libnuma1=2.0.14-3 libopenmpi-dev=4.1.4-1 libopenmpi3=4.1.4-1 libp11-kit0=0.24.1-1 libpam-modules=1.4.0-13 libpam-modules-bin=1.4.0-13 libpam-runtime=1.4.0-13 libpam0g=1.4.0-13 libpciaccess0=0.16-3 libpcre2-8-0=10.40-1 libpcre3=2:8.39-14 libperl5.34=5.34.0-4 libpipeline1=1.5.6-1 libpmix-dev=4.1.2-2 libpmix2=4.1.2-2 libprocps8=2:3.3.17-7+b1 libpsl5=0.21.0-1.2 libpsm-infinipath1=3.3+20.604758e7-6.1 libpsm2-2=11.2.185-1 libpython3-dev=3.10.4-1+b1 libpython3-stdlib=3.10.4-1+b1 libpython3.10=3.10.4-4+b1 libpython3.10-dev=3.10.4-4+b1 libpython3.10-minimal=3.10.4-4+b1 libpython3.10-stdlib=3.10.4-4+b1 libquadmath0=12.1.0-2 librbio2=1:5.12.0+dfsg-1 librdmacm1=40.0-1 libreadline8=8.1.2-1.2 librhash0=1.4.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.28+dfsg-6 libsasl2-modules-db=2.1.28+dfsg-6 libseccomp2=2.5.4-1 libselinux1=3.3-1+b2 libsemanage-common=3.3-1 libsemanage2=3.3-1+b2 libsepol2=3.3-1 libsigsegv2=2.14-1 libsliplu1=1:5.12.0+dfsg-1 libsmartcols1=2.38-4 libspqr2=1:5.12.0+dfsg-1 libsqlite3-0=3.38.5-1 libssh2-1=1.10.0-3+b1 libssl3=3.0.3-5 libstdc++-11-dev=11.3.0-3 libstdc++6=12.1.0-2 libsub-override-perl=0.09-2 libsuitesparse-dev=1:5.12.0+dfsg-1 libsuitesparseconfig5=1:5.12.0+dfsg-1 libsuperlu-dev=5.3.0+dfsg1-2 libsuperlu5=5.3.0+dfsg1-2 libsystemd0=251.1-1 libtasn1-6=4.18.0-4 libtinfo6=6.3+20220423-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.7-4 libtsan0=11.3.0-3 libtsan2=12.1.0-2 libubsan1=12.1.0-2 libuchardet0=0.0.7-1 libucx0=1.13.0~rc1-1 libudev1=251.1-1 libumfpack5=1:5.12.0+dfsg-1 libunicode-escape-perl=0.0.2-4.1 libunicode-string-perl=2.10-1+b7 libunistring2=1.0-1 libuuid1=2.38-4 libuv1=1.44.1-2 libx11-6=2:1.7.5-1 libx11-data=2:1.7.5-1 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxml2=2.9.14+dfsg-1 libxnvctrl0=470.103.01-2 libyaml-0-2=0.2.2-1 libzstd1=1.5.2+dfsg-1 linux-libc-dev=5.17.11-1 login=1:4.11.1+dfsg1-2 lsb-base=11.2 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 media-types=8.0.0 mpi-default-dev=1.14 ncurses-base=6.3+20220423-2 ncurses-bin=6.3+20220423-2 ocl-icd-libopencl1=2.2.14-3 openmpi-bin=4.1.4-1 openmpi-common=4.1.4-1 openssh-client=1:9.0p1-1+b1 openssl=3.0.3-5 passwd=1:4.11.1+dfsg1-2 patch=2.7.6-7 perl=5.34.0-4 perl-base=5.34.0-4 perl-modules-5.34=5.34.0-4 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 procps=2:3.3.17-7+b1 pybind11-dev=2.9.2-1 pybuild-plugin-pyproject=5.20220403 python-babel-localedata=2.8.0+dfsg.1-7 python3=3.10.4-1+b1 python3-alabaster=0.7.12-1 python3-babel=2.8.0+dfsg.1-7 python3-build=0.7.0-3 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-2 python3-charset-normalizer=2.0.6-2 python3-dev=3.10.4-1+b1 python3-distutils=3.9.12-1 python3-docutils=0.17.1+dfsg-2 python3-idna=3.3-1 python3-imagesize=1.3.0-1 python3-importlib-metadata=4.6.4-1 python3-installer=0.5.1+dfsg1-1 python3-jinja2=3.0.3-1 python3-lib2to3=3.9.12-1 python3-markupsafe=2.0.1-2+b1 python3-minimal=3.10.4-1+b1 python3-more-itertools=8.10.0-2 python3-packaging=21.3-1 python3-pep517=0.12.0-1 python3-pkg-resources=59.6.0-1.2 python3-pybind11=2.9.2-1 python3-pygments=2.11.2+dfsg-2 python3-pyparsing=3.0.7-2 python3-requests=2.27.1+dfsg-1 python3-roman=3.3-1 python3-setuptools=59.6.0-1.2 python3-six=1.16.0-3 python3-snowballstemmer=2.2.0-1 python3-sphinx=4.5.0-3 python3-sphinx-rtd-theme=1.0.0+dfsg-1 python3-toml=0.10.2-1 python3-tomli=1.2.2-2 python3-tz=2022.1-1 python3-urllib3=1.26.9-1 python3-wheel=0.37.1-2 python3-yaml=5.4.1-1+b1 python3-zipp=1.0.0-3 python3.10=3.10.4-4+b1 python3.10-dev=3.10.4-4+b1 python3.10-minimal=3.10.4-4+b1 readline-common=8.1.2-1.2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sgml-base=1.30 sphinx-common=4.5.0-3 sphinx-rtd-theme-common=1.0.0+dfsg-1 swig=4.0.2-2 swig4.0=4.0.2-2 sysvinit-utils=3.03-1 tar=1.34+dfsg-1 tzdata=2022a-1 util-linux=2.38-4 util-linux-extra=2.38-4 xml-core=0.18+nmu1 xz-utils=5.2.5-2.1 zlib1g=1:1.2.11.dfsg-4 zlib1g-dev=1:1.2.11.dfsg-4 --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/20220531T085056Z/ unstable main deb-src http://snapshot.notset.fr/archive/debian/20220531T085056Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220603T205729Z/ 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 apbs=3.4.1-2 && mkdir -p /build/apbs-A5U5s9 && dpkg-source --no-check -x /*.dsc /build/apbs-A5U5s9/apbs-3.4.1 && chown -R builduser:builduser /build/apbs-A5U5s9" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/apbs-A5U5s9/apbs-3.4.1 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1653958367" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/apbs-A5U5s9 /tmp/apbs-3.4.1-2clh41mvc bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220603T205729Z 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.CAmx4OZ2M0 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.CAmx4OZ2M0 Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 136 kB of archives. After this operation, 401 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220603T205729Z unstable/main amd64 libfakeroot amd64 1.29-1 [48.5 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220603T205729Z unstable/main amd64 fakeroot amd64 1.29-1 [87.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 136 kB in 0s (764 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 ... 4629 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.29-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.29-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.29-1_amd64.deb ... Unpacking fakeroot (1.29-1) ... Setting up libfakeroot:amd64 (1.29-1) ... Setting up fakeroot (1.29-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... 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/20220531T085056Z/ unstable main deb-src http://snapshot.notset.fr/archive/debian/20220531T085056Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220603T205729Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.CAmx4OZ2M0 Get:1 http://snapshot.notset.fr/archive/debian/20220531T085056Z unstable InRelease [165 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20220603T205729Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20220531T085056Z unstable/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220531T085056Z unstable/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220531T085056Z unstable/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220531T085056Z unstable/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220531T085056Z unstable/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220531T085056Z unstable/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20220531T085056Z unstable/main Sources [13.0 MB] Get:4 http://snapshot.notset.fr/archive/debian/20220531T085056Z unstable/main amd64 Packages [12.5 MB] Fetched 25.6 MB in 22s (1179 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.CAmx4OZ2M0 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d apbs=3.4.1-2 && mkdir -p /build/apbs-A5U5s9 && dpkg-source --no-check -x /*.dsc /build/apbs-A5U5s9/apbs-3.4.1 && chown -R builduser:builduser /build/apbs-A5U5s9"' exec /tmp/mmdebstrap.CAmx4OZ2M0 Reading package lists... NOTICE: 'apbs' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/apbs.git Please use: git clone https://salsa.debian.org/debichem-team/apbs.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 106 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220531T085056Z unstable/main apbs 3.4.1-2 (dsc) [2639 B] Get:2 http://snapshot.notset.fr/archive/debian/20220531T085056Z unstable/main apbs 3.4.1-2 (tar) [85.8 MB] Get:3 http://snapshot.notset.fr/archive/debian/20220531T085056Z unstable/main apbs 3.4.1-2 (diff) [20.3 MB] Fetched 106 MB in 1min 23s (1282 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'apbs_3.4.1-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting apbs in /build/apbs-A5U5s9/apbs-3.4.1 dpkg-source: info: unpacking apbs_3.4.1.orig.tar.gz dpkg-source: info: unpacking apbs_3.4.1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying wrong-path-for-interpreter.patch dpkg-source: info: applying debian_testfiles.patch dpkg-source: info: applying fix_spelling_errors.patch dpkg-source: info: applying shared_library_soname.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying cmake.patch dpkg-source: info: applying docs.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/apbs-A5U5s9/apbs-3.4.1 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1653958367" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.CAmx4OZ2M0 dpkg-buildpackage: info: source package apbs dpkg-buildpackage: info: source version 3.4.1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source --before-build . fakeroot debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=cmake dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules build-indep dh build-indep --with python3,sphinxdoc --buildsystem=cmake dh_update_autotools_config -i -O--buildsystem=cmake dh_autoreconf -i -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1' dh_auto_configure -- \ -DCMAKE_BUILD_TYPE=None \ -DAPBS_STATIC_BUILD=Off \ -DBUILD_DOC=Off -DBUILD_TOOLS=On \ -DENABLE_OPENMP=On -DENABLE_MPI=On \ -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On \ -DENABLE_READLINE=Off -DENABLE_ZLIB=On \ -DFETCHCONTENT_SOURCE_DIR_FETK=/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk \ -DRPC_CFLAGS=-I/usr/include/tirpc \ -DBUILD_MALOC=Off cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCMAKE_BUILD_TYPE=None -DAPBS_STATIC_BUILD=Off -DBUILD_DOC=Off -DBUILD_TOOLS=On -DENABLE_OPENMP=On -DENABLE_MPI=On -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On -DENABLE_READLINE=Off -DENABLE_ZLIB=On -DFETCHCONTENT_SOURCE_DIR_FETK=/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk -DRPC_CFLAGS=-I/usr/include/tirpc -DBUILD_MALOC=Off .. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- 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 -- Install prefix: /usr -- -- APBS Static build: Off -- Building shared libs: ON -- Find-library suffixes: .so;.so;.a -- -- Building FETK from commit 57195e55351e04ce6ee0ef56a143c996a9aee7e2 -- FETK set_basic_vars_and_paths: FALSE, FETK -- Setting project paths -- Install prefix: /usr -- FETK static build: OFF -- Building shared libs: ON -- Find-library suffixes: .so;.so;.so;.a Configuring build for PUNC -- FETK set_basic_vars_and_paths: FALSE, punc -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of mode_t -- Check size of mode_t - done -- Check size of pid_t -- Check size of pid_t - done -- Check size of size_t -- Check size of size_t - done -- Looking for 4 include files stdlib.h, ..., float.h -- Looking for 4 include files stdlib.h, ..., float.h - found -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file sys/socket.h -- Looking for include file sys/socket.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file sys/un.h -- Looking for include file sys/un.h - found -- Looking for include file sys/wait.h -- Looking for include file sys/wait.h - found -- Looking for include file netinet/in.h -- Looking for include file netinet/in.h - found -- Looking for include file arpa/inet.h -- Looking for include file arpa/inet.h - found -- Looking for include file netdb.h -- Looking for include file netdb.h - found -- Looking for include file sys/stat.h -- Looking for include file sys/stat.h - found -- Looking for include file fcntl.h -- Looking for include file fcntl.h - found -- Looking for include file rpc/rpc.h -- Looking for include file rpc/rpc.h - found -- Looking for getcwd -- Looking for getcwd - found -- Looking for O_NONBLOCK -- Looking for O_NONBLOCK - found -- Will build vf2c -- Looking for sgemm_ -- Looking for sgemm_ - not 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 sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test SUPERLU_HAS_GLOBAL_MEM_USAGE_T -- Performing Test SUPERLU_HAS_GLOBAL_MEM_USAGE_T - Success -- Performing Test SUPERLU_HAS_CLEAN_ENUMS -- Performing Test SUPERLU_HAS_CLEAN_ENUMS - Success -- Performing Test SUPERLU_HAS_GLOBALLU_T -- Performing Test SUPERLU_HAS_GLOBALLU_T - Success -- Found SuperLU: /usr/include/superlu (found version "5.0") -- Found ARPACK: libraries at /usr/lib/x86_64-linux-gnu/libarpack.so -- Will build CGCODE -- Building vf2c -- Type: EXTERNAL_HEADERS -- Items: punc/varpack.h;punc/vblas.h;punc/vcgcode.h;punc/vlapack.h;punc/vpmg.h;punc/vf2c.h -- Type: INTERNAL_HEADERS -- Items: f2c.h;fio.h;fmt.h;fp.h;lio.h;rawio.h;signal1.h;sysdep1.h -- Type: SOURCES -- Items: f77vers.c;i77vers.c;s_rnge.c;abort_.c;exit_.c;getarg_.c;iargc_.c;getenv_.c;signal_.c;s_stop.c;s_paus.c;system_.c;cabs.c;derf_.c;derfc_.c;erf_.c;erfc_.c;sig_die.c;uninit.c;pow_ci.c;pow_dd.c;pow_di.c;pow_hh.c;pow_ii.c;pow_ri.c;pow_zi.c;pow_zz.c;c_abs.c;c_cos.c;c_div.c;c_exp.c;c_log.c;c_sin.c;c_sqrt.c;z_abs.c;z_cos.c;z_div.c;z_exp.c;z_log.c;z_sin.c;z_sqrt.c;r_abs.c;r_acos.c;r_asin.c;r_atan.c;r_atn2.c;r_cnjg.c;r_cos.c;r_cosh.c;r_dim.c;r_exp.c;r_imag.c;r_int.c;r_lg10.c;r_log.c;r_mod.c;r_nint.c;r_sign.c;r_sin.c;r_sinh.c;r_sqrt.c;r_tan.c;r_tanh.c;d_abs.c;d_acos.c;d_asin.c;d_atan.c;d_atn2.c;d_cnjg.c;d_cos.c;d_cosh.c;d_dim.c;d_exp.c;d_imag.c;d_int.c;d_lg10.c;d_log.c;d_mod.c;d_nint.c;d_prod.c;d_sign.c;d_sin.c;d_sinh.c;d_sqrt.c;d_tan.c;d_tanh.c;i_abs.c;i_dim.c;i_dnnt.c;i_indx.c;i_len.c;i_mod.c;i_nint.c;i_sign.c;lbitbits.c;lbitshft.c;h_abs.c;h_dim.c;h_dnnt.c;h_indx.c;h_len.c;h_mod.c;h_nint.c;h_sign.c;l_ge.c;l_gt.c;l_le.c;l_lt.c;hl_ge.c;hl_gt.c;hl_le.c;hl_lt.c;ef1asc_.c;ef1cmc_.c;f77_aloc.c;s_cat.c;s_cmp.c;s_copy.c;dtime_.c;etime_.c;backspac.c;close.c;dfe.c;dolio.c;due.c;endfile.c;err.c;fmt.c;fmtlib.c;ftell_.c;iio.c;ilnw.c;inquire.c;lread.c;lwrite.c;open.c;rdfmt.c;rewind.c;rsfe.c;rsli.c;rsne.c;sfe.c;sue.c;typesize.c;uio.c;util.c;wref.c;wrtfmt.c;wsfe.c;wsle.c;wsne.c;xwsne.c;main.c -- Building cgcode -- Type: INTERNAL_HEADERS -- Items: vcgcode.h -- Type: SOURCES -- Items: scgdrv.c;scg.c;scr.c;scrind.c;spcg.c;scgnr.c;scgne.c;spcgnr.c;spcgne.c;sppcg.c;spcgca.c;sdpchb.c;scbfix.c;sckchb.c;scgchk.c;sonest.c;msstop.c;r1mach.c;sratqr.c;dcgdrv.c;dcg.c;dcr.c;dcrind.c;dpcg.c;dcgnr.c;dcgne.c;dpcgnr.c;dpcgne.c;dppcg.c;dpcgca.c;ddpchb.c;dcbfix.c;dckchb.c;dcgchk.c;donest.c;mdstop.c;d1mach.c;dratqr.c;depsln.c -- Type: INTERNAL_HEADERS -- Items: /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/punccf.h -- Type: SOURCES -- Items: punc_base.c -- Type: EXTERNAL_HEADERS -- Items: punc/punc.h;punc/punc_base.h -- Type: INTERNAL_HEADERS -- Items: punc_base_p.h Configuring build for GAMER -- FETK set_basic_vars_and_paths: FALSE, gamer -- Type: INTERNAL_HEADERS -- Items: /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src/gamercf.h -- Type: SOURCES -- Items: gamer_base.c -- Type: EXTERNAL_HEADERS -- Items: gamer/gamer.h;gamer/gamer_base.h -- Type: INTERNAL_HEADERS -- Items: gamer_base_p.h -- Type: SOURCES -- Items: triangle.c -- Type: EXTERNAL_HEADERS -- Items: gamer/triangle.h -- Type: INTERNAL_HEADERS -- Items: triangle_p.h -- Type: SOURCES -- Items: predicates.cpp;tetgen.cpp -- Type: EXTERNAL_HEADERS -- Items: gamer/tetgen.h -- Type: INTERNAL_HEADERS -- Items: tetgen_p.h -- Type: SOURCES -- Items: CorrectNormals.C;GenerateSphereMesh.C;MarchingCube.C;PDB2Mesh.C;PDB2Volume.C;ReadLattice.C;ReadPDB.C;ReadWriteMesh.C;RegionGrowing.C;SurfaceMesh.C;SurfExtract.C;SurfRefine.C;SurfSmooth.C -- Type: EXTERNAL_HEADERS -- Items: gamer/biom.h -- Type: INTERNAL_HEADERS -- Items: MarchingCube.h;PDB2Volume.h Configuring build for MC -- FETK set_basic_vars_and_paths: FALSE, mc -- Found UMFPACK: /usr/include/suitesparse -- @@@@ finding blas -- @@@@ finding lapack -- %%%%% list of libraries: -- Testing libraries: TRUE -- CMAKE_REQUIRED_LIBRARIES: /usr/lib/x86_64-linux-gnu/libblas.so;-lpthread;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- Found LAPACK: /usr/lib/x86_64-linux-gnu/libblas.so;-lpthread;-lm;-ldl -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/x86_64-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/x86_64-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/x86_64-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/x86_64-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/x86_64-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/x86_64-linux-gnu/libspqr.so -- Did not find Intel TBB library, assuming SuiteSparseQR was not compiled with TBB. -- @@@@ finding config -- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse -- Found SUITESPARSE_CONFIG library: /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/x86_64-linux-gnu/librt.so -- Adding librt: /usr/lib/x86_64-linux-gnu/librt.so to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing). -- @@@@ finding metis -- Did not find METIS library (optional SuiteSparse dependency) -- Found SuiteSparse: TRUE (found version "5.12.0") -- Type: INTERNAL_HEADERS -- Items: /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src/mccf.h -- Type: SOURCES -- Items: mc_base.c -- Type: EXTERNAL_HEADERS -- Items: mc/mc_base.h;mc/mc.h -- Type: INTERNAL_HEADERS -- Items: mc_base_p.h -- Type: SOURCES -- Items: bmat.c;bsolv.c;bvec.c;mat.c;matcopy.c;matln.c;mtool.c;slu.c;vec.c;vec3.c;zslu.c -- Type: EXTERNAL_HEADERS -- Items: mc/bam.h;mc/bmat.h;mc/bvec.h;mc/mat.h;mc/mtool.h;mc/slu.h;mc/vec.h;mc/vec3.h;mc/zslu.h -- Type: INTERNAL_HEADERS -- Items: bam_p.h;bmat_p.h;bvec_p.h;mat_p.h;mtool_p.h;slu_p.h;vec_p.h;vec3_p.h;zslu_p.h -- Type: SOURCES -- Items: whb.c;bvechb.c;hbtools.c;rcmat.c;brcmat.c;subopt.c -- Type: EXTERNAL_HEADERS -- Items: mc/whb.h -- Type: INTERNAL_HEADERS -- Items: brcmat_p.h;bvechb_p.h;cholesky_p.h;hbtools_p.h;rcmat_p.h;subopt_p.h;whb_p.h -- Type: SOURCES -- Items: aprx.c;assem.c;bnode.c;estim.c;eval.c;io.c;node.c;parti.c;re.c -- Type: EXTERNAL_HEADERS -- Items: mc/aprx.h;mc/bnode.h;mc/node.h;mc/re.h -- Type: INTERNAL_HEADERS -- Items: aprx_p.h;bnode_p.h;node_p.h;re_p.h -- Type: SOURCES -- Items: vel.c;ves.c;gem.c;gemchk.c;gemdisp.c;gemg.c;gemgen.c;gemio.c;gemref.c;gemunref.c;gemcube.c -- Type: EXTERNAL_HEADERS -- Items: mc/gem.h;mc/vel.h;mc/ves.h -- Type: INTERNAL_HEADERS -- Items: gem_p.h;vel_p.h;ves_p.h -- Type: SOURCES -- Items: pde.c -- Type: EXTERNAL_HEADERS -- Items: mc/pde.h -- Type: INTERNAL_HEADERS -- Items: pde_p.h -- Type: SOURCES -- Items: am.c;lsolv.c;nsolv.c -- Type: EXTERNAL_HEADERS -- Items: mc/am.h;mc/nam.h -- Type: INTERNAL_HEADERS -- Items: am_p.h;nam_p.h -- Type: SOURCES -- Items: dyn.c;svio.c -- Type: EXTERNAL_HEADERS -- Items: mc/dyn.h -- Type: INTERNAL_HEADERS -- Items: dyn_p.h;svio_p.h -- Type: SOURCES -- Items: mcsh.c -- Type: EXTERNAL_HEADERS -- Items: mc/mcsh.h -- Type: INTERNAL_HEADERS -- Items: mcsh_p.h -- ############################################################# -- ** PROJECT NAME: APBS -- ** PROJECT DESC: Adaptive Poisson-Boltzmann Solver -- ** PROJECT URL: http://www.poissonboltzmann.org/ -- ** VERSION_DATA: 3.4.1 -- ** CURRENT_TIME: 2022-05-31T00:52:47 -- ** CURRENT_YEAR: 2022 -- Setting project paths -- Setting lookup paths for headers and libraries -- Computing machine epsilon values -- Floating point epsilon is 2.220446e-16 -- Double precision epsilon is 2.220446e-16 -- Looking for time -- Looking for time - found -- Looking for rand -- Looking for rand - found -- Looking for srand -- Looking for srand - found -- Found Intl: built in to C library -- Performing Test Iconv_IS_BUILT_IN -- Performing Test Iconv_IS_BUILT_IN - Success -- Found Iconv: built in to C library -- @@@@ finding blas -- @@@@ finding lapack -- %%%%% list of libraries: -- Testing libraries: TRUE -- CMAKE_REQUIRED_LIBRARIES: /usr/lib/x86_64-linux-gnu/libblas.so;-lpthread;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/x86_64-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/x86_64-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/x86_64-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/x86_64-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/x86_64-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/x86_64-linux-gnu/libspqr.so -- Did not find Intel TBB library, assuming SuiteSparseQR was not compiled with TBB. -- @@@@ finding config -- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse -- Found SUITESPARSE_CONFIG library: /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/x86_64-linux-gnu/librt.so -- Adding librt: /usr/lib/x86_64-linux-gnu/librt.so to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing). -- @@@@ finding metis -- Did not find METIS library (optional SuiteSparse dependency) -- UMFPack libraries: /usr/lib/x86_64-linux-gnu/libumfpack.so -- SUITESPARSE_INCLUDE_DIRS: /usr/include/suitesparse -- SUITESPARSE_LIBRARIES: /usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lpthread;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.so -- Checking for MPI -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI support enabled -- Inline functions enabled -- Verbose debugging mode enabled -- Checking for OpenMP -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- OpenMP support enabled -- Building of iAPBS interface disabled -- Adding apbs_generic -- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c -- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;-lpthread;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lpthread;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Added apbs_generic -- Adding apbs_pmgc -- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c -- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;-lpthread;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lpthread;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Added apbs_pmgc -- Adding apbs_mg -- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c -- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;-lpthread;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lpthread;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic;apbs_pmgc -- Added apbs_mg -- Adding apbs_fem -- With source files vcsm.c;vfetk.c;vpee.c -- With external header files vcsm.h;vfetk.h;vpee.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;-lpthread;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lpthread;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic -- Added apbs_fem -- Adding apbs_routines -- With source files routines.c -- With external header files -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;-lpthread;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lpthread;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;mc;util;dl;m;stdc++;-lpthread;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lpthread;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic;apbs_pmgc;apbs_mg;apbs_fem -- Added apbs_routines -- External Headers: -- -- APBS Libraries: mc;util;dl;m;stdc++;-lpthread;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lpthread;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines -- -- -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -- Supplemental tools enabled -- Building mesh -- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines -- Building manip -- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines CMake Deprecation Warning at tools/python/CMakeLists.txt:2 (CMAKE_POLICY): The OLD behavior for policy CMP0078 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. CMake Deprecation Warning at tools/python/CMakeLists.txt:3 (CMAKE_POLICY): The OLD behavior for policy CMP0086 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Found SWIG: /usr/bin/swig4.0 (found version "4.0.2") -- Found Python3: /usr/bin/python3.10 (found suitable version "3.10.4", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- ***** Python3 include path is: /usr/include/python3.10 -- ***** Python3 library path is: /usr/lib/x86_64-linux-gnu/libpython3.10.so -- ***** Python3 library dir is: /usr/lib/x86_64-linux-gnu CMake Warning at /usr/lib/cmake/pybind11/pybind11Tools.cmake:24 (message): Set PYBIND11_PYTHON_VERSION to search for a specific version, not PYTHON_VERSION (which is an output). Assuming that is what you meant to do and continuing anyway. Call Stack (most recent call first): /usr/lib/cmake/pybind11/pybind11Common.cmake:206 (include) /usr/lib/cmake/pybind11/pybind11Config.cmake:250 (include) tools/python-pybind/CMakeLists.txt:2 (find_package) -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.10.4", minimum required is "3.6") -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.10.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/include (found version "2.9.2") -- LIBS mc;util;dl;m;stdc++;-lpthread;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lpthread;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- INTERNAL_LIBS apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines -- ******* TESTING ADDED ***************** -- Found Python3: /usr/bin/python3.10 (found suitable exact version "3.10.4") found components: Interpreter -- ******* FOUND TEST CASE born, born -- TEST born_test WORKING_DIRECTORY /build/apbs-A5U5s9/apbs-3.4.1/tests COMMAND /usr/bin/python3.10 /build/apbs-A5U5s9/apbs-3.4.1/tests/apbs_tester.py -e apbs -t born -- ******* FOUND TEST CASE actin, actin-dimer-auto -- TEST actin-dimer-auto_test WORKING_DIRECTORY /build/apbs-A5U5s9/apbs-3.4.1/tests COMMAND /usr/bin/python3.10 /build/apbs-A5U5s9/apbs-3.4.1/tests/apbs_tester.py -e apbs -t actin-dimer-auto -- ******* FOUND TEST CASE alkanes, alkanes -- TEST alkanes_test WORKING_DIRECTORY /build/apbs-A5U5s9/apbs-3.4.1/tests COMMAND /usr/bin/python3.10 /build/apbs-A5U5s9/apbs-3.4.1/tests/apbs_tester.py -e apbs -t alkanes -- ******* FOUND TEST CASE FKBP, FKBP -- TEST FKBP_test WORKING_DIRECTORY /build/apbs-A5U5s9/apbs-3.4.1/tests COMMAND /usr/bin/python3.10 /build/apbs-A5U5s9/apbs-3.4.1/tests/apbs_tester.py -e apbs -t FKBP -- ******* FOUND TEST CASE hca, hca-bind -- TEST hca-bind_test WORKING_DIRECTORY /build/apbs-A5U5s9/apbs-3.4.1/tests COMMAND /usr/bin/python3.10 /build/apbs-A5U5s9/apbs-3.4.1/tests/apbs_tester.py -e apbs -t hca-bind -- ******* FOUND TEST CASE ionize, ionize -- TEST ionize_test WORKING_DIRECTORY /build/apbs-A5U5s9/apbs-3.4.1/tests COMMAND /usr/bin/python3.10 /build/apbs-A5U5s9/apbs-3.4.1/tests/apbs_tester.py -e apbs -t ionize -- ******* FOUND TEST CASE ion, ion-pmf -- TEST ion-pmf_test WORKING_DIRECTORY /build/apbs-A5U5s9/apbs-3.4.1/tests COMMAND /usr/bin/python3.10 /build/apbs-A5U5s9/apbs-3.4.1/tests/apbs_tester.py -e apbs -t ion-pmf -- ******* FOUND TEST CASE pka, pka-lig -- TEST pka-lig_test WORKING_DIRECTORY /build/apbs-A5U5s9/apbs-3.4.1/tests COMMAND /usr/bin/python3.10 /build/apbs-A5U5s9/apbs-3.4.1/tests/apbs_tester.py -e apbs -t pka-lig -- ******* FOUND TEST CASE point, point-pmf -- TEST point-pmf_test WORKING_DIRECTORY /build/apbs-A5U5s9/apbs-3.4.1/tests COMMAND /usr/bin/python3.10 /build/apbs-A5U5s9/apbs-3.4.1/tests/apbs_tester.py -e apbs -t point-pmf -- ******* FOUND TEST CASE solv, solv -- TEST solv_test WORKING_DIRECTORY /build/apbs-A5U5s9/apbs-3.4.1/tests COMMAND /usr/bin/python3.10 /build/apbs-A5U5s9/apbs-3.4.1/tests/apbs_tester.py -e apbs -t solv -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY ENABLE_READLINE ENABLE_ZLIB -- Build files have been written to: /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1' dh_auto_build -i -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/apbs-A5U5s9/apbs-3.4.1 -B/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/CMakeFiles /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build.make _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depend make -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/depend make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/depend make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/python /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build make -f _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build.make _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build Dependee "/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake" is newer than depender "/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend.internal". Dependee "/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend.internal". make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' Scanning dependencies of target apbslib_swig_compilation make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/build [ 1%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/base/gamer_base.c.o [ 1%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/triangle/triangle.c.o [ 1%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 1%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgdrv.c.o [ 1%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/base/gamer_base.c.o -MF CMakeFiles/gamer.dir/base/gamer_base.c.o.d -o CMakeFiles/gamer.dir/base/gamer_base.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base/gamer_base.c [ 2%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgdrv.c.o -MF CMakeFiles/cgcode.dir/scgdrv.c.o.d -o CMakeFiles/cgcode.dir/scgdrv.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgdrv.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/triangle/triangle.c.o -MF CMakeFiles/gamer.dir/triangle/triangle.c.o.d -o CMakeFiles/gamer.dir/triangle/triangle.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle/triangle.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o -MF CMakeFiles/gamer.dir/tetgen/predicates.cpp.o.d -o CMakeFiles/gamer.dir/tetgen/predicates.cpp.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/predicates.cpp cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o -MF CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o.d -o CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o -MF CMakeFiles/gamer.dir/biom/CorrectNormals.C.o.d -o CMakeFiles/gamer.dir/biom/CorrectNormals.C.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/CorrectNormals.C [ 2%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77vers.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77vers.c.o -MF CMakeFiles/vf2c.dir/f77vers.c.o.d -o CMakeFiles/vf2c.dir/f77vers.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/f77vers.c [ 2%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o -MF CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o.d -o CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/GenerateSphereMesh.C [ 3%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scg.c.o [ 3%] Swig compile apbslib.i for python cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scg.c.o -MF CMakeFiles/cgcode.dir/scg.c.o.d -o CMakeFiles/cgcode.dir/scg.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scg.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E make_directory /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E touch /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON.stamp [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i77vers.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i77vers.c.o -MF CMakeFiles/vf2c.dir/i77vers.c.o.d -o CMakeFiles/vf2c.dir/i77vers.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i77vers.c [ 4%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o -MF CMakeFiles/gamer.dir/biom/MarchingCube.C.o.d -o CMakeFiles/gamer.dir/biom/MarchingCube.C.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/MarchingCube.C cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E env SWIG_LIB=/usr/share/swig4.0 /usr/bin/swig4.0 -python -outdir /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python -interface _apbslib -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/python3.10 -I/build/apbs-A5U5s9/apbs-3.4.1/tools/python -o /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c /build/apbs-A5U5s9/apbs-3.4.1/tools/python/apbslib.i [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_rnge.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_rnge.c.o -MF CMakeFiles/vf2c.dir/s_rnge.c.o.d -o CMakeFiles/vf2c.dir/s_rnge.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_rnge.c [ 4%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scr.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scr.c.o -MF CMakeFiles/cgcode.dir/scr.c.o.d -o CMakeFiles/cgcode.dir/scr.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scr.c [ 4%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scrind.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scrind.c.o -MF CMakeFiles/cgcode.dir/scrind.c.o.d -o CMakeFiles/cgcode.dir/scrind.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scrind.c [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/abort_.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/abort_.c.o -MF CMakeFiles/vf2c.dir/abort_.c.o.d -o CMakeFiles/vf2c.dir/abort_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/abort_.c [ 5%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/exit_.c.o [ 5%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcg.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/exit_.c.o -MF CMakeFiles/vf2c.dir/exit_.c.o.d -o CMakeFiles/vf2c.dir/exit_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/exit_.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcg.c.o -MF CMakeFiles/cgcode.dir/spcg.c.o.d -o CMakeFiles/cgcode.dir/spcg.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcg.c [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getarg_.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getarg_.c.o -MF CMakeFiles/vf2c.dir/getarg_.c.o.d -o CMakeFiles/vf2c.dir/getarg_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/getarg_.c [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgnr.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgnr.c.o -MF CMakeFiles/cgcode.dir/scgnr.c.o.d -o CMakeFiles/cgcode.dir/scgnr.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgnr.c [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iargc_.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iargc_.c.o -MF CMakeFiles/vf2c.dir/iargc_.c.o.d -o CMakeFiles/vf2c.dir/iargc_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/iargc_.c [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgne.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgne.c.o -MF CMakeFiles/cgcode.dir/scgne.c.o.d -o CMakeFiles/cgcode.dir/scgne.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgne.c [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getenv_.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getenv_.c.o -MF CMakeFiles/vf2c.dir/getenv_.c.o.d -o CMakeFiles/vf2c.dir/getenv_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/getenv_.c [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgnr.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgnr.c.o -MF CMakeFiles/cgcode.dir/spcgnr.c.o.d -o CMakeFiles/cgcode.dir/spcgnr.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgnr.c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function ‘void tetgenmesh::constrainedfacets()’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20804:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20804 | equatptlist = new list("point *"); | ^~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20809:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20809 | horizptlist = new list("point *"); | ^~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20810:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20810 | belowptlist = new list("point *"); | ^~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20811:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20811 | aboveptlist = new list("point *"); | ^~~~~~~~~ [ 7%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o -MF CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o.d -o CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Mesh.C [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/signal_.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/signal_.c.o -MF CMakeFiles/vf2c.dir/signal_.c.o.d -o CMakeFiles/vf2c.dir/signal_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/signal_.c make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 8%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o [ 9%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgne.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o -MF CMakeFiles/gamer.dir/biom/PDB2Volume.C.o.d -o CMakeFiles/gamer.dir/biom/PDB2Volume.C.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgne.c.o -MF CMakeFiles/cgcode.dir/spcgne.c.o.d -o CMakeFiles/cgcode.dir/spcgne.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgne.c [ 9%] Built target apbslib_swig_compilation /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function ‘long int tetgenmesh::reconstructmesh()’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:24383:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 24383 | markerlist = new list("int"); | ^~~~~ [ 9%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o -MF CMakeFiles/cgcode.dir/sppcg.c.o.d -o CMakeFiles/cgcode.dir/sppcg.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sppcg.c [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_stop.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_stop.c.o -MF CMakeFiles/vf2c.dir/s_stop.c.o.d -o CMakeFiles/vf2c.dir/s_stop.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_stop.c [ 9%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgca.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgca.c.o -MF CMakeFiles/cgcode.dir/spcgca.c.o.d -o CMakeFiles/cgcode.dir/spcgca.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgca.c [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sdpchb.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sdpchb.c.o -MF CMakeFiles/cgcode.dir/sdpchb.c.o.d -o CMakeFiles/cgcode.dir/sdpchb.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sdpchb.c [ 10%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_paus.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_paus.c.o -MF CMakeFiles/vf2c.dir/s_paus.c.o.d -o CMakeFiles/vf2c.dir/s_paus.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_paus.c [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scbfix.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scbfix.c.o -MF CMakeFiles/cgcode.dir/scbfix.c.o.d -o CMakeFiles/cgcode.dir/scbfix.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scbfix.c [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sckchb.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sckchb.c.o -MF CMakeFiles/cgcode.dir/sckchb.c.o.d -o CMakeFiles/cgcode.dir/sckchb.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sckchb.c [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o -MF CMakeFiles/cgcode.dir/scgchk.c.o.d -o CMakeFiles/cgcode.dir/scgchk.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgchk.c [ 11%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o -MF CMakeFiles/cgcode.dir/sonest.c.o.d -o CMakeFiles/cgcode.dir/sonest.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sonest.c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C: In function ‘float PDB2Volume(char*, float**, int*, int*, int*, float*, float*, ATOM**, int*, char)’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C:85:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85 | fscanf(fp,"%d\n",&m); | ~~~~~~^~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C:88:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | fscanf(fp,"%f %f %f %f\n",&x,&y,&z,&radius); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/system_.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/system_.c.o -MF CMakeFiles/vf2c.dir/system_.c.o.d -o CMakeFiles/vf2c.dir/system_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/system_.c [ 11%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o [ 11%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/msstop.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o -MF CMakeFiles/cgcode.dir/r1mach.c.o.d -o CMakeFiles/cgcode.dir/r1mach.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/r1mach.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/msstop.c.o -MF CMakeFiles/cgcode.dir/msstop.c.o.d -o CMakeFiles/cgcode.dir/msstop.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/msstop.c [ 12%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o -MF CMakeFiles/cgcode.dir/sratqr.c.o.d -o CMakeFiles/cgcode.dir/sratqr.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sratqr.c [ 12%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o -MF CMakeFiles/cgcode.dir/dcgdrv.c.o.d -o CMakeFiles/cgcode.dir/dcgdrv.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgdrv.c [ 13%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o [ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/cabs.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o -MF CMakeFiles/cgcode.dir/dcg.c.o.d -o CMakeFiles/cgcode.dir/dcg.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcg.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/cabs.c.o -MF CMakeFiles/vf2c.dir/cabs.c.o.d -o CMakeFiles/vf2c.dir/cabs.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/cabs.c [ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derf_.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derf_.c.o -MF CMakeFiles/vf2c.dir/derf_.c.o.d -o CMakeFiles/vf2c.dir/derf_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/derf_.c [ 13%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o -MF CMakeFiles/cgcode.dir/dcr.c.o.d -o CMakeFiles/cgcode.dir/dcr.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcr.c [ 14%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o [ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o -MF CMakeFiles/cgcode.dir/dcrind.c.o.d -o CMakeFiles/cgcode.dir/dcrind.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcrind.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o -MF CMakeFiles/vf2c.dir/derfc_.c.o.d -o CMakeFiles/vf2c.dir/derfc_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/derfc_.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erf_.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erf_.c.o -MF CMakeFiles/vf2c.dir/erf_.c.o.d -o CMakeFiles/vf2c.dir/erf_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/erf_.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erfc_.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erfc_.c.o -MF CMakeFiles/vf2c.dir/erfc_.c.o.d -o CMakeFiles/vf2c.dir/erfc_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/erfc_.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sig_die.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sig_die.c.o -MF CMakeFiles/vf2c.dir/sig_die.c.o.d -o CMakeFiles/vf2c.dir/sig_die.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sig_die.c [ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o -MF CMakeFiles/cgcode.dir/dpcg.c.o.d -o CMakeFiles/cgcode.dir/dpcg.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcg.c [ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o -MF CMakeFiles/cgcode.dir/dcgne.c.o.d -o CMakeFiles/cgcode.dir/dcgne.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgne.c [ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgnr.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgnr.c.o -MF CMakeFiles/cgcode.dir/dcgnr.c.o.d -o CMakeFiles/cgcode.dir/dcgnr.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgnr.c [ 16%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgnr.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgnr.c.o -MF CMakeFiles/cgcode.dir/dpcgnr.c.o.d -o CMakeFiles/cgcode.dir/dpcgnr.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgnr.c [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uninit.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uninit.c.o -MF CMakeFiles/vf2c.dir/uninit.c.o.d -o CMakeFiles/vf2c.dir/uninit.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/uninit.c [ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ci.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ci.c.o -MF CMakeFiles/vf2c.dir/pow_ci.c.o.d -o CMakeFiles/vf2c.dir/pow_ci.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ci.c [ 17%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o -MF CMakeFiles/cgcode.dir/dpcgne.c.o.d -o CMakeFiles/cgcode.dir/dpcgne.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgne.c [ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_dd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_dd.c.o -MF CMakeFiles/vf2c.dir/pow_dd.c.o.d -o CMakeFiles/vf2c.dir/pow_dd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_dd.c [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgca.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgca.c.o -MF CMakeFiles/cgcode.dir/dpcgca.c.o.d -o CMakeFiles/cgcode.dir/dpcgca.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgca.c [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o -MF CMakeFiles/cgcode.dir/dppcg.c.o.d -o CMakeFiles/cgcode.dir/dppcg.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dppcg.c [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/ddpchb.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/ddpchb.c.o -MF CMakeFiles/cgcode.dir/ddpchb.c.o.d -o CMakeFiles/cgcode.dir/ddpchb.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/ddpchb.c [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_di.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_di.c.o -MF CMakeFiles/vf2c.dir/pow_di.c.o.d -o CMakeFiles/vf2c.dir/pow_di.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_di.c [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o -MF CMakeFiles/cgcode.dir/dcbfix.c.o.d -o CMakeFiles/cgcode.dir/dcbfix.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcbfix.c [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o -MF CMakeFiles/cgcode.dir/dckchb.c.o.d -o CMakeFiles/cgcode.dir/dckchb.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dckchb.c [ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgchk.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgchk.c.o -MF CMakeFiles/cgcode.dir/dcgchk.c.o.d -o CMakeFiles/cgcode.dir/dcgchk.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgchk.c [ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o -MF CMakeFiles/cgcode.dir/donest.c.o.d -o CMakeFiles/cgcode.dir/donest.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/donest.c [ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o -MF CMakeFiles/cgcode.dir/mdstop.c.o.d -o CMakeFiles/cgcode.dir/mdstop.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/mdstop.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o -MF CMakeFiles/vf2c.dir/pow_hh.c.o.d -o CMakeFiles/vf2c.dir/pow_hh.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_hh.c [ 20%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o -MF CMakeFiles/cgcode.dir/d1mach.c.o.d -o CMakeFiles/cgcode.dir/d1mach.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/d1mach.c [ 20%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o [ 20%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depsln.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o -MF CMakeFiles/cgcode.dir/dratqr.c.o.d -o CMakeFiles/cgcode.dir/dratqr.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dratqr.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depsln.c.o -MF CMakeFiles/cgcode.dir/depsln.c.o.d -o CMakeFiles/cgcode.dir/depsln.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/depsln.c [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ri.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ri.c.o -MF CMakeFiles/vf2c.dir/pow_ri.c.o.d -o CMakeFiles/vf2c.dir/pow_ri.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ri.c [ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o -MF CMakeFiles/vf2c.dir/pow_ii.c.o.d -o CMakeFiles/vf2c.dir/pow_ii.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ii.c [ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zi.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zi.c.o -MF CMakeFiles/vf2c.dir/pow_zi.c.o.d -o CMakeFiles/vf2c.dir/pow_zi.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_zi.c [ 22%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadLattice.C.o [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zz.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadLattice.C.o -MF CMakeFiles/gamer.dir/biom/ReadLattice.C.o.d -o CMakeFiles/gamer.dir/biom/ReadLattice.C.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadLattice.C cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zz.c.o -MF CMakeFiles/vf2c.dir/pow_zz.c.o.d -o CMakeFiles/vf2c.dir/pow_zz.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_zz.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_abs.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_abs.c.o -MF CMakeFiles/vf2c.dir/c_abs.c.o.d -o CMakeFiles/vf2c.dir/c_abs.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_abs.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_cos.c.o [ 22%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_cos.c.o -MF CMakeFiles/vf2c.dir/c_cos.c.o.d -o CMakeFiles/vf2c.dir/c_cos.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_cos.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o -MF CMakeFiles/gamer.dir/biom/ReadPDB.C.o.d -o CMakeFiles/gamer.dir/biom/ReadPDB.C.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadPDB.C [ 23%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o [ 23%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o -MF CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o.d -o CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o -MF CMakeFiles/gamer.dir/biom/RegionGrowing.C.o.d -o CMakeFiles/gamer.dir/biom/RegionGrowing.C.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/RegionGrowing.C [ 23%] Linking C shared library libcgcode.so cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cmake -E cmake_link_script CMakeFiles/cgcode.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libcgcode.so.1.9 -o libcgcode.so.1.9.3 CMakeFiles/cgcode.dir/scgdrv.c.o CMakeFiles/cgcode.dir/scg.c.o CMakeFiles/cgcode.dir/scr.c.o CMakeFiles/cgcode.dir/scrind.c.o CMakeFiles/cgcode.dir/spcg.c.o CMakeFiles/cgcode.dir/scgnr.c.o CMakeFiles/cgcode.dir/scgne.c.o CMakeFiles/cgcode.dir/spcgnr.c.o CMakeFiles/cgcode.dir/spcgne.c.o CMakeFiles/cgcode.dir/sppcg.c.o CMakeFiles/cgcode.dir/spcgca.c.o CMakeFiles/cgcode.dir/sdpchb.c.o CMakeFiles/cgcode.dir/scbfix.c.o CMakeFiles/cgcode.dir/sckchb.c.o CMakeFiles/cgcode.dir/scgchk.c.o CMakeFiles/cgcode.dir/sonest.c.o CMakeFiles/cgcode.dir/msstop.c.o CMakeFiles/cgcode.dir/r1mach.c.o CMakeFiles/cgcode.dir/sratqr.c.o CMakeFiles/cgcode.dir/dcgdrv.c.o CMakeFiles/cgcode.dir/dcg.c.o CMakeFiles/cgcode.dir/dcr.c.o CMakeFiles/cgcode.dir/dcrind.c.o CMakeFiles/cgcode.dir/dpcg.c.o CMakeFiles/cgcode.dir/dcgnr.c.o CMakeFiles/cgcode.dir/dcgne.c.o CMakeFiles/cgcode.dir/dpcgnr.c.o CMakeFiles/cgcode.dir/dpcgne.c.o CMakeFiles/cgcode.dir/dppcg.c.o CMakeFiles/cgcode.dir/dpcgca.c.o CMakeFiles/cgcode.dir/ddpchb.c.o CMakeFiles/cgcode.dir/dcbfix.c.o CMakeFiles/cgcode.dir/dckchb.c.o CMakeFiles/cgcode.dir/dcgchk.c.o CMakeFiles/cgcode.dir/donest.c.o CMakeFiles/cgcode.dir/mdstop.c.o CMakeFiles/cgcode.dir/d1mach.c.o CMakeFiles/cgcode.dir/dratqr.c.o CMakeFiles/cgcode.dir/depsln.c.o [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_div.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_div.c.o -MF CMakeFiles/vf2c.dir/c_div.c.o.d -o CMakeFiles/vf2c.dir/c_div.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_div.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o -MF CMakeFiles/vf2c.dir/c_exp.c.o.d -o CMakeFiles/vf2c.dir/c_exp.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_exp.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cmake -E cmake_symlink_library libcgcode.so.1.9.3 libcgcode.so.1.9 libcgcode.so [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o -MF CMakeFiles/vf2c.dir/c_log.c.o.d -o CMakeFiles/vf2c.dir/c_log.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_log.c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function ‘SurfaceMesh* SurfaceMesh_readOFF(char*)’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:401:14: warning: too many arguments for format [-Wformat-extra-args] 401 | printf("Read error. Expected 3 integers for the first simplex.\n", n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:494:14: warning: too many arguments for format [-Wformat-extra-args] 494 | printf("Read error. Expected 4 integers for the first simplex.\n", n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function ‘GemMesh* GemMesh_fromSurfaceMesh(SurfaceMesh*, char*)’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:754:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 754 | in.save_nodes("plc"); | ^~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:755:16: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 755 | in.save_poly("plc"); | ^~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:761:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 761 | out.save_nodes("result"); | ^~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:762:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 762 | out.save_elements("result"); | ^~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:763:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 763 | out.save_faces("result"); | ^~~~~~~~ make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 24%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o -MF CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o.d -o CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfaceMesh.C [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o -MF CMakeFiles/vf2c.dir/c_sin.c.o.d -o CMakeFiles/vf2c.dir/c_sin.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_sin.c [ 25%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o -MF CMakeFiles/gamer.dir/biom/SurfExtract.C.o.d -o CMakeFiles/gamer.dir/biom/SurfExtract.C.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfExtract.C [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sqrt.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sqrt.c.o -MF CMakeFiles/vf2c.dir/c_sqrt.c.o.d -o CMakeFiles/vf2c.dir/c_sqrt.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_sqrt.c [ 26%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o -MF CMakeFiles/gamer.dir/biom/SurfRefine.C.o.d -o CMakeFiles/gamer.dir/biom/SurfRefine.C.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfRefine.C [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o -MF CMakeFiles/vf2c.dir/z_abs.c.o.d -o CMakeFiles/vf2c.dir/z_abs.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_abs.c [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o -MF CMakeFiles/vf2c.dir/z_cos.c.o.d -o CMakeFiles/vf2c.dir/z_cos.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_cos.c [ 26%] Built target cgcode [ 26%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfSmooth.C.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -MF CMakeFiles/gamer.dir/biom/SurfSmooth.C.o.d -o CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfSmooth.C [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o -MF CMakeFiles/vf2c.dir/z_div.c.o.d -o CMakeFiles/vf2c.dir/z_div.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_div.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o -MF CMakeFiles/vf2c.dir/z_exp.c.o.d -o CMakeFiles/vf2c.dir/z_exp.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_exp.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o -MF CMakeFiles/vf2c.dir/z_log.c.o.d -o CMakeFiles/vf2c.dir/z_log.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_log.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o -MF CMakeFiles/vf2c.dir/z_sin.c.o.d -o CMakeFiles/vf2c.dir/z_sin.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_sin.c [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o -MF CMakeFiles/vf2c.dir/r_abs.c.o.d -o CMakeFiles/vf2c.dir/r_abs.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_abs.c [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o -MF CMakeFiles/vf2c.dir/z_sqrt.c.o.d -o CMakeFiles/vf2c.dir/z_sqrt.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_sqrt.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o -MF CMakeFiles/vf2c.dir/r_acos.c.o.d -o CMakeFiles/vf2c.dir/r_acos.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_acos.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o -MF CMakeFiles/vf2c.dir/r_asin.c.o.d -o CMakeFiles/vf2c.dir/r_asin.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_asin.c [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o -MF CMakeFiles/vf2c.dir/r_atan.c.o.d -o CMakeFiles/vf2c.dir/r_atan.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_atan.c [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atn2.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atn2.c.o -MF CMakeFiles/vf2c.dir/r_atn2.c.o.d -o CMakeFiles/vf2c.dir/r_atn2.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_atn2.c [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o -MF CMakeFiles/vf2c.dir/r_cnjg.c.o.d -o CMakeFiles/vf2c.dir/r_cnjg.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cnjg.c [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cos.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cos.c.o -MF CMakeFiles/vf2c.dir/r_cos.c.o.d -o CMakeFiles/vf2c.dir/r_cos.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cos.c [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cosh.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cosh.c.o -MF CMakeFiles/vf2c.dir/r_cosh.c.o.d -o CMakeFiles/vf2c.dir/r_cosh.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cosh.c [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_dim.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_dim.c.o -MF CMakeFiles/vf2c.dir/r_dim.c.o.d -o CMakeFiles/vf2c.dir/r_dim.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_dim.c [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_exp.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_exp.c.o -MF CMakeFiles/vf2c.dir/r_exp.c.o.d -o CMakeFiles/vf2c.dir/r_exp.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_exp.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_int.c.o [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_imag.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_int.c.o -MF CMakeFiles/vf2c.dir/r_int.c.o.d -o CMakeFiles/vf2c.dir/r_int.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_int.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_imag.c.o -MF CMakeFiles/vf2c.dir/r_imag.c.o.d -o CMakeFiles/vf2c.dir/r_imag.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_imag.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_log.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_log.c.o -MF CMakeFiles/vf2c.dir/r_log.c.o.d -o CMakeFiles/vf2c.dir/r_log.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_log.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_lg10.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_lg10.c.o -MF CMakeFiles/vf2c.dir/r_lg10.c.o.d -o CMakeFiles/vf2c.dir/r_lg10.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_lg10.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_nint.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_nint.c.o -MF CMakeFiles/vf2c.dir/r_nint.c.o.d -o CMakeFiles/vf2c.dir/r_nint.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_nint.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sign.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sign.c.o -MF CMakeFiles/vf2c.dir/r_sign.c.o.d -o CMakeFiles/vf2c.dir/r_sign.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sign.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_mod.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_mod.c.o -MF CMakeFiles/vf2c.dir/r_mod.c.o.d -o CMakeFiles/vf2c.dir/r_mod.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_mod.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sqrt.c.o [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sinh.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sqrt.c.o -MF CMakeFiles/vf2c.dir/r_sqrt.c.o.d -o CMakeFiles/vf2c.dir/r_sqrt.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sqrt.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sinh.c.o -MF CMakeFiles/vf2c.dir/r_sinh.c.o.d -o CMakeFiles/vf2c.dir/r_sinh.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sinh.c [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sin.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sin.c.o -MF CMakeFiles/vf2c.dir/r_sin.c.o.d -o CMakeFiles/vf2c.dir/r_sin.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sin.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tan.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tan.c.o -MF CMakeFiles/vf2c.dir/r_tan.c.o.d -o CMakeFiles/vf2c.dir/r_tan.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_tan.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o -MF CMakeFiles/vf2c.dir/d_abs.c.o.d -o CMakeFiles/vf2c.dir/d_abs.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_abs.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tanh.c.o [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tanh.c.o -MF CMakeFiles/vf2c.dir/r_tanh.c.o.d -o CMakeFiles/vf2c.dir/r_tanh.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_tanh.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o -MF CMakeFiles/vf2c.dir/d_asin.c.o.d -o CMakeFiles/vf2c.dir/d_asin.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_asin.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o -MF CMakeFiles/vf2c.dir/d_acos.c.o.d -o CMakeFiles/vf2c.dir/d_acos.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_acos.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atan.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atan.c.o -MF CMakeFiles/vf2c.dir/d_atan.c.o.d -o CMakeFiles/vf2c.dir/d_atan.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_atan.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atn2.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atn2.c.o -MF CMakeFiles/vf2c.dir/d_atn2.c.o.d -o CMakeFiles/vf2c.dir/d_atn2.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_atn2.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o -MF CMakeFiles/vf2c.dir/d_cnjg.c.o.d -o CMakeFiles/vf2c.dir/d_cnjg.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cnjg.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o -MF CMakeFiles/vf2c.dir/d_cosh.c.o.d -o CMakeFiles/vf2c.dir/d_cosh.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cosh.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_dim.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_dim.c.o -MF CMakeFiles/vf2c.dir/d_dim.c.o.d -o CMakeFiles/vf2c.dir/d_dim.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_dim.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o -MF CMakeFiles/vf2c.dir/d_cos.c.o.d -o CMakeFiles/vf2c.dir/d_cos.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cos.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_exp.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o -MF CMakeFiles/vf2c.dir/d_imag.c.o.d -o CMakeFiles/vf2c.dir/d_imag.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_imag.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_exp.c.o -MF CMakeFiles/vf2c.dir/d_exp.c.o.d -o CMakeFiles/vf2c.dir/d_exp.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_exp.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o -MF CMakeFiles/vf2c.dir/d_lg10.c.o.d -o CMakeFiles/vf2c.dir/d_lg10.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_lg10.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_int.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_int.c.o -MF CMakeFiles/vf2c.dir/d_int.c.o.d -o CMakeFiles/vf2c.dir/d_int.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_int.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_log.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_log.c.o -MF CMakeFiles/vf2c.dir/d_log.c.o.d -o CMakeFiles/vf2c.dir/d_log.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_log.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_mod.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_mod.c.o -MF CMakeFiles/vf2c.dir/d_mod.c.o.d -o CMakeFiles/vf2c.dir/d_mod.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_mod.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o -MF CMakeFiles/vf2c.dir/d_nint.c.o.d -o CMakeFiles/vf2c.dir/d_nint.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_nint.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sin.c.o [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sign.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sin.c.o -MF CMakeFiles/vf2c.dir/d_sin.c.o.d -o CMakeFiles/vf2c.dir/d_sin.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sin.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sign.c.o -MF CMakeFiles/vf2c.dir/d_sign.c.o.d -o CMakeFiles/vf2c.dir/d_sign.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sign.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_prod.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_prod.c.o -MF CMakeFiles/vf2c.dir/d_prod.c.o.d -o CMakeFiles/vf2c.dir/d_prod.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_prod.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o -MF CMakeFiles/vf2c.dir/d_sqrt.c.o.d -o CMakeFiles/vf2c.dir/d_sqrt.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sqrt.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sinh.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sinh.c.o -MF CMakeFiles/vf2c.dir/d_sinh.c.o.d -o CMakeFiles/vf2c.dir/d_sinh.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sinh.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o -MF CMakeFiles/vf2c.dir/d_tanh.c.o.d -o CMakeFiles/vf2c.dir/d_tanh.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_tanh.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o -MF CMakeFiles/vf2c.dir/i_dim.c.o.d -o CMakeFiles/vf2c.dir/i_dim.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_dim.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o -MF CMakeFiles/vf2c.dir/d_tan.c.o.d -o CMakeFiles/vf2c.dir/d_tan.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_tan.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o -MF CMakeFiles/vf2c.dir/i_dnnt.c.o.d -o CMakeFiles/vf2c.dir/i_dnnt.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_dnnt.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o -MF CMakeFiles/vf2c.dir/i_abs.c.o.d -o CMakeFiles/vf2c.dir/i_abs.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_abs.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o -MF CMakeFiles/vf2c.dir/i_indx.c.o.d -o CMakeFiles/vf2c.dir/i_indx.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_indx.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_len.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_len.c.o -MF CMakeFiles/vf2c.dir/i_len.c.o.d -o CMakeFiles/vf2c.dir/i_len.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_len.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_mod.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_mod.c.o -MF CMakeFiles/vf2c.dir/i_mod.c.o.d -o CMakeFiles/vf2c.dir/i_mod.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_mod.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_nint.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_nint.c.o -MF CMakeFiles/vf2c.dir/i_nint.c.o.d -o CMakeFiles/vf2c.dir/i_nint.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_nint.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitshft.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitshft.c.o -MF CMakeFiles/vf2c.dir/lbitshft.c.o.d -o CMakeFiles/vf2c.dir/lbitshft.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lbitshft.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_sign.c.o [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitbits.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_sign.c.o -MF CMakeFiles/vf2c.dir/i_sign.c.o.d -o CMakeFiles/vf2c.dir/i_sign.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_sign.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitbits.c.o -MF CMakeFiles/vf2c.dir/lbitbits.c.o.d -o CMakeFiles/vf2c.dir/lbitbits.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lbitbits.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_abs.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_abs.c.o -MF CMakeFiles/vf2c.dir/h_abs.c.o.d -o CMakeFiles/vf2c.dir/h_abs.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_abs.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dim.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dim.c.o -MF CMakeFiles/vf2c.dir/h_dim.c.o.d -o CMakeFiles/vf2c.dir/h_dim.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_dim.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o -MF CMakeFiles/vf2c.dir/h_indx.c.o.d -o CMakeFiles/vf2c.dir/h_indx.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_indx.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dnnt.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dnnt.c.o -MF CMakeFiles/vf2c.dir/h_dnnt.c.o.d -o CMakeFiles/vf2c.dir/h_dnnt.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_dnnt.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_mod.c.o [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_mod.c.o -MF CMakeFiles/vf2c.dir/h_mod.c.o.d -o CMakeFiles/vf2c.dir/h_mod.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_mod.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o -MF CMakeFiles/vf2c.dir/h_nint.c.o.d -o CMakeFiles/vf2c.dir/h_nint.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_nint.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_len.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_len.c.o -MF CMakeFiles/vf2c.dir/h_len.c.o.d -o CMakeFiles/vf2c.dir/h_len.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_len.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o -MF CMakeFiles/vf2c.dir/h_sign.c.o.d -o CMakeFiles/vf2c.dir/h_sign.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_sign.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o -MF CMakeFiles/vf2c.dir/l_ge.c.o.d -o CMakeFiles/vf2c.dir/l_ge.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_ge.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o -MF CMakeFiles/vf2c.dir/l_gt.c.o.d -o CMakeFiles/vf2c.dir/l_gt.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_gt.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o -MF CMakeFiles/vf2c.dir/l_lt.c.o.d -o CMakeFiles/vf2c.dir/l_lt.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_lt.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o -MF CMakeFiles/vf2c.dir/l_le.c.o.d -o CMakeFiles/vf2c.dir/l_le.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_le.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o -MF CMakeFiles/vf2c.dir/hl_ge.c.o.d -o CMakeFiles/vf2c.dir/hl_ge.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_ge.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_gt.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_gt.c.o -MF CMakeFiles/vf2c.dir/hl_gt.c.o.d -o CMakeFiles/vf2c.dir/hl_gt.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_gt.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_le.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_le.c.o -MF CMakeFiles/vf2c.dir/hl_le.c.o.d -o CMakeFiles/vf2c.dir/hl_le.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_le.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_lt.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_lt.c.o -MF CMakeFiles/vf2c.dir/hl_lt.c.o.d -o CMakeFiles/vf2c.dir/hl_lt.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_lt.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77_aloc.c.o [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1cmc_.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77_aloc.c.o -MF CMakeFiles/vf2c.dir/f77_aloc.c.o.d -o CMakeFiles/vf2c.dir/f77_aloc.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/f77_aloc.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1cmc_.c.o -MF CMakeFiles/vf2c.dir/ef1cmc_.c.o.d -o CMakeFiles/vf2c.dir/ef1cmc_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ef1cmc_.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1asc_.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1asc_.c.o -MF CMakeFiles/vf2c.dir/ef1asc_.c.o.d -o CMakeFiles/vf2c.dir/ef1asc_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ef1asc_.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cat.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cat.c.o -MF CMakeFiles/vf2c.dir/s_cat.c.o.d -o CMakeFiles/vf2c.dir/s_cat.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_cat.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cmp.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cmp.c.o -MF CMakeFiles/vf2c.dir/s_cmp.c.o.d -o CMakeFiles/vf2c.dir/s_cmp.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_cmp.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_copy.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_copy.c.o -MF CMakeFiles/vf2c.dir/s_copy.c.o.d -o CMakeFiles/vf2c.dir/s_copy.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_copy.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/backspac.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/backspac.c.o -MF CMakeFiles/vf2c.dir/backspac.c.o.d -o CMakeFiles/vf2c.dir/backspac.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/etime_.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/etime_.c.o -MF CMakeFiles/vf2c.dir/etime_.c.o.d -o CMakeFiles/vf2c.dir/etime_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/etime_.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/close.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/close.c.o -MF CMakeFiles/vf2c.dir/close.c.o.d -o CMakeFiles/vf2c.dir/close.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/close.c [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dtime_.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dtime_.c.o -MF CMakeFiles/vf2c.dir/dtime_.c.o.d -o CMakeFiles/vf2c.dir/dtime_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/dtime_.c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c: In function ‘f_back’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c:47:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 47 | fread((char *)&n,sizeof(uiolen),1,f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dfe.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dfe.c.o -MF CMakeFiles/vf2c.dir/dfe.c.o.d -o CMakeFiles/vf2c.dir/dfe.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/dfe.c [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dolio.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dolio.c.o -MF CMakeFiles/vf2c.dir/dolio.c.o.d -o CMakeFiles/vf2c.dir/dolio.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/dolio.c [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/due.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/due.c.o -MF CMakeFiles/vf2c.dir/due.c.o.d -o CMakeFiles/vf2c.dir/due.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/due.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/endfile.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/endfile.c.o -MF CMakeFiles/vf2c.dir/endfile.c.o.d -o CMakeFiles/vf2c.dir/endfile.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/endfile.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/err.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/err.c.o -MF CMakeFiles/vf2c.dir/err.c.o.d -o CMakeFiles/vf2c.dir/err.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/err.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmt.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmt.c.o -MF CMakeFiles/vf2c.dir/fmt.c.o.d -o CMakeFiles/vf2c.dir/fmt.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/fmt.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmtlib.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmtlib.c.o -MF CMakeFiles/vf2c.dir/fmtlib.c.o.d -o CMakeFiles/vf2c.dir/fmtlib.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/fmtlib.c [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ftell_.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ftell_.c.o -MF CMakeFiles/vf2c.dir/ftell_.c.o.d -o CMakeFiles/vf2c.dir/ftell_.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ftell_.c [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iio.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iio.c.o -MF CMakeFiles/vf2c.dir/iio.c.o.d -o CMakeFiles/vf2c.dir/iio.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/iio.c [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ilnw.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ilnw.c.o -MF CMakeFiles/vf2c.dir/ilnw.c.o.d -o CMakeFiles/vf2c.dir/ilnw.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ilnw.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/inquire.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/inquire.c.o -MF CMakeFiles/vf2c.dir/inquire.c.o.d -o CMakeFiles/vf2c.dir/inquire.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/inquire.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lread.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lread.c.o -MF CMakeFiles/vf2c.dir/lread.c.o.d -o CMakeFiles/vf2c.dir/lread.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lread.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lwrite.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lwrite.c.o -MF CMakeFiles/vf2c.dir/lwrite.c.o.d -o CMakeFiles/vf2c.dir/lwrite.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lwrite.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rdfmt.c.o [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rdfmt.c.o -MF CMakeFiles/vf2c.dir/rdfmt.c.o.d -o CMakeFiles/vf2c.dir/rdfmt.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rdfmt.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o -MF CMakeFiles/vf2c.dir/open.c.o.d -o CMakeFiles/vf2c.dir/open.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/open.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o -MF CMakeFiles/vf2c.dir/rewind.c.o.d -o CMakeFiles/vf2c.dir/rewind.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rewind.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsfe.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsfe.c.o -MF CMakeFiles/vf2c.dir/rsfe.c.o.d -o CMakeFiles/vf2c.dir/rsfe.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rsfe.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsli.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsli.c.o -MF CMakeFiles/vf2c.dir/rsli.c.o.d -o CMakeFiles/vf2c.dir/rsli.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rsli.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsne.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsne.c.o -MF CMakeFiles/vf2c.dir/rsne.c.o.d -o CMakeFiles/vf2c.dir/rsne.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rsne.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sfe.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sfe.c.o -MF CMakeFiles/vf2c.dir/sfe.c.o.d -o CMakeFiles/vf2c.dir/sfe.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sfe.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sue.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sue.c.o -MF CMakeFiles/vf2c.dir/sue.c.o.d -o CMakeFiles/vf2c.dir/sue.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sue.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/util.c.o [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/util.c.o -MF CMakeFiles/vf2c.dir/util.c.o.d -o CMakeFiles/vf2c.dir/util.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/util.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uio.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o -MF CMakeFiles/vf2c.dir/typesize.c.o.d -o CMakeFiles/vf2c.dir/typesize.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/typesize.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uio.c.o -MF CMakeFiles/vf2c.dir/uio.c.o.d -o CMakeFiles/vf2c.dir/uio.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/uio.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wref.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wref.c.o -MF CMakeFiles/vf2c.dir/wref.c.o.d -o CMakeFiles/vf2c.dir/wref.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wref.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wrtfmt.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wrtfmt.c.o -MF CMakeFiles/vf2c.dir/wrtfmt.c.o.d -o CMakeFiles/vf2c.dir/wrtfmt.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wrtfmt.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsfe.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsfe.c.o -MF CMakeFiles/vf2c.dir/wsfe.c.o.d -o CMakeFiles/vf2c.dir/wsfe.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsfe.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsle.c.o [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsne.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsne.c.o -MF CMakeFiles/vf2c.dir/wsne.c.o.d -o CMakeFiles/vf2c.dir/wsne.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsne.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsle.c.o -MF CMakeFiles/vf2c.dir/wsle.c.o.d -o CMakeFiles/vf2c.dir/wsle.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsle.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/xwsne.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/xwsne.c.o -MF CMakeFiles/vf2c.dir/xwsne.c.o.d -o CMakeFiles/vf2c.dir/xwsne.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/xwsne.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/main.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/main.c.o -MF CMakeFiles/vf2c.dir/main.c.o.d -o CMakeFiles/vf2c.dir/main.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/main.c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/main.c:115:1: warning: return type defaults to ‘int’ [-Wimplicit-int] 115 | main(int argc, char **argv) | ^~~~ [ 60%] Linking C shared library libvf2c.so cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cmake -E cmake_link_script CMakeFiles/vf2c.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libvf2c.so.1.9 -o libvf2c.so.1.9.3 CMakeFiles/vf2c.dir/f77vers.c.o CMakeFiles/vf2c.dir/i77vers.c.o CMakeFiles/vf2c.dir/s_rnge.c.o CMakeFiles/vf2c.dir/abort_.c.o CMakeFiles/vf2c.dir/exit_.c.o CMakeFiles/vf2c.dir/getarg_.c.o CMakeFiles/vf2c.dir/iargc_.c.o CMakeFiles/vf2c.dir/getenv_.c.o CMakeFiles/vf2c.dir/signal_.c.o CMakeFiles/vf2c.dir/s_stop.c.o CMakeFiles/vf2c.dir/s_paus.c.o CMakeFiles/vf2c.dir/system_.c.o CMakeFiles/vf2c.dir/cabs.c.o CMakeFiles/vf2c.dir/derf_.c.o CMakeFiles/vf2c.dir/derfc_.c.o CMakeFiles/vf2c.dir/erf_.c.o CMakeFiles/vf2c.dir/erfc_.c.o CMakeFiles/vf2c.dir/sig_die.c.o CMakeFiles/vf2c.dir/uninit.c.o CMakeFiles/vf2c.dir/pow_ci.c.o CMakeFiles/vf2c.dir/pow_dd.c.o CMakeFiles/vf2c.dir/pow_di.c.o CMakeFiles/vf2c.dir/pow_hh.c.o CMakeFiles/vf2c.dir/pow_ii.c.o CMakeFiles/vf2c.dir/pow_ri.c.o CMakeFiles/vf2c.dir/pow_zi.c.o CMakeFiles/vf2c.dir/pow_zz.c.o CMakeFiles/vf2c.dir/c_abs.c.o CMakeFiles/vf2c.dir/c_cos.c.o CMakeFiles/vf2c.dir/c_div.c.o CMakeFiles/vf2c.dir/c_exp.c.o CMakeFiles/vf2c.dir/c_log.c.o CMakeFiles/vf2c.dir/c_sin.c.o CMakeFiles/vf2c.dir/c_sqrt.c.o CMakeFiles/vf2c.dir/z_abs.c.o CMakeFiles/vf2c.dir/z_cos.c.o CMakeFiles/vf2c.dir/z_div.c.o CMakeFiles/vf2c.dir/z_exp.c.o CMakeFiles/vf2c.dir/z_log.c.o CMakeFiles/vf2c.dir/z_sin.c.o CMakeFiles/vf2c.dir/z_sqrt.c.o CMakeFiles/vf2c.dir/r_abs.c.o CMakeFiles/vf2c.dir/r_acos.c.o CMakeFiles/vf2c.dir/r_asin.c.o CMakeFiles/vf2c.dir/r_atan.c.o CMakeFiles/vf2c.dir/r_atn2.c.o CMakeFiles/vf2c.dir/r_cnjg.c.o CMakeFiles/vf2c.dir/r_cos.c.o CMakeFiles/vf2c.dir/r_cosh.c.o CMakeFiles/vf2c.dir/r_dim.c.o CMakeFiles/vf2c.dir/r_exp.c.o CMakeFiles/vf2c.dir/r_imag.c.o CMakeFiles/vf2c.dir/r_int.c.o CMakeFiles/vf2c.dir/r_lg10.c.o CMakeFiles/vf2c.dir/r_log.c.o CMakeFiles/vf2c.dir/r_mod.c.o CMakeFiles/vf2c.dir/r_nint.c.o CMakeFiles/vf2c.dir/r_sign.c.o CMakeFiles/vf2c.dir/r_sin.c.o CMakeFiles/vf2c.dir/r_sinh.c.o CMakeFiles/vf2c.dir/r_sqrt.c.o CMakeFiles/vf2c.dir/r_tan.c.o CMakeFiles/vf2c.dir/r_tanh.c.o CMakeFiles/vf2c.dir/d_abs.c.o CMakeFiles/vf2c.dir/d_acos.c.o CMakeFiles/vf2c.dir/d_asin.c.o CMakeFiles/vf2c.dir/d_atan.c.o CMakeFiles/vf2c.dir/d_atn2.c.o CMakeFiles/vf2c.dir/d_cnjg.c.o CMakeFiles/vf2c.dir/d_cos.c.o CMakeFiles/vf2c.dir/d_cosh.c.o CMakeFiles/vf2c.dir/d_dim.c.o CMakeFiles/vf2c.dir/d_exp.c.o CMakeFiles/vf2c.dir/d_imag.c.o CMakeFiles/vf2c.dir/d_int.c.o CMakeFiles/vf2c.dir/d_lg10.c.o CMakeFiles/vf2c.dir/d_log.c.o CMakeFiles/vf2c.dir/d_mod.c.o CMakeFiles/vf2c.dir/d_nint.c.o CMakeFiles/vf2c.dir/d_prod.c.o CMakeFiles/vf2c.dir/d_sign.c.o CMakeFiles/vf2c.dir/d_sin.c.o CMakeFiles/vf2c.dir/d_sinh.c.o CMakeFiles/vf2c.dir/d_sqrt.c.o CMakeFiles/vf2c.dir/d_tan.c.o CMakeFiles/vf2c.dir/d_tanh.c.o CMakeFiles/vf2c.dir/i_abs.c.o CMakeFiles/vf2c.dir/i_dim.c.o CMakeFiles/vf2c.dir/i_dnnt.c.o CMakeFiles/vf2c.dir/i_indx.c.o CMakeFiles/vf2c.dir/i_len.c.o CMakeFiles/vf2c.dir/i_mod.c.o CMakeFiles/vf2c.dir/i_nint.c.o CMakeFiles/vf2c.dir/i_sign.c.o CMakeFiles/vf2c.dir/lbitbits.c.o CMakeFiles/vf2c.dir/lbitshft.c.o CMakeFiles/vf2c.dir/h_abs.c.o CMakeFiles/vf2c.dir/h_dim.c.o CMakeFiles/vf2c.dir/h_dnnt.c.o CMakeFiles/vf2c.dir/h_indx.c.o CMakeFiles/vf2c.dir/h_len.c.o CMakeFiles/vf2c.dir/h_mod.c.o CMakeFiles/vf2c.dir/h_nint.c.o CMakeFiles/vf2c.dir/h_sign.c.o CMakeFiles/vf2c.dir/l_ge.c.o CMakeFiles/vf2c.dir/l_gt.c.o CMakeFiles/vf2c.dir/l_le.c.o CMakeFiles/vf2c.dir/l_lt.c.o CMakeFiles/vf2c.dir/hl_ge.c.o CMakeFiles/vf2c.dir/hl_gt.c.o CMakeFiles/vf2c.dir/hl_le.c.o CMakeFiles/vf2c.dir/hl_lt.c.o CMakeFiles/vf2c.dir/ef1asc_.c.o CMakeFiles/vf2c.dir/ef1cmc_.c.o CMakeFiles/vf2c.dir/f77_aloc.c.o CMakeFiles/vf2c.dir/s_cat.c.o CMakeFiles/vf2c.dir/s_cmp.c.o CMakeFiles/vf2c.dir/s_copy.c.o CMakeFiles/vf2c.dir/dtime_.c.o CMakeFiles/vf2c.dir/etime_.c.o CMakeFiles/vf2c.dir/backspac.c.o CMakeFiles/vf2c.dir/close.c.o CMakeFiles/vf2c.dir/dfe.c.o CMakeFiles/vf2c.dir/dolio.c.o CMakeFiles/vf2c.dir/due.c.o CMakeFiles/vf2c.dir/endfile.c.o CMakeFiles/vf2c.dir/err.c.o CMakeFiles/vf2c.dir/fmt.c.o CMakeFiles/vf2c.dir/fmtlib.c.o CMakeFiles/vf2c.dir/ftell_.c.o CMakeFiles/vf2c.dir/iio.c.o CMakeFiles/vf2c.dir/ilnw.c.o CMakeFiles/vf2c.dir/inquire.c.o CMakeFiles/vf2c.dir/lread.c.o CMakeFiles/vf2c.dir/lwrite.c.o CMakeFiles/vf2c.dir/open.c.o CMakeFiles/vf2c.dir/rdfmt.c.o CMakeFiles/vf2c.dir/rewind.c.o CMakeFiles/vf2c.dir/rsfe.c.o CMakeFiles/vf2c.dir/rsli.c.o CMakeFiles/vf2c.dir/rsne.c.o CMakeFiles/vf2c.dir/sfe.c.o CMakeFiles/vf2c.dir/sue.c.o CMakeFiles/vf2c.dir/typesize.c.o CMakeFiles/vf2c.dir/uio.c.o CMakeFiles/vf2c.dir/util.c.o CMakeFiles/vf2c.dir/wref.c.o CMakeFiles/vf2c.dir/wrtfmt.c.o CMakeFiles/vf2c.dir/wsfe.c.o CMakeFiles/vf2c.dir/wsle.c.o CMakeFiles/vf2c.dir/wsne.c.o CMakeFiles/vf2c.dir/xwsne.c.o CMakeFiles/vf2c.dir/main.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cmake -E cmake_symlink_library libvf2c.so.1.9.3 libvf2c.so.1.9 libvf2c.so make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 60%] Built target vf2c make -f _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build.make _deps/fetk-build/punc/src/CMakeFiles/punc.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/CMakeFiles/punc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build.make _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 60%] Building C object _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cc -Dpunc_EXPORTS -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o -MF CMakeFiles/punc.dir/base/punc_base.c.o.d -o CMakeFiles/punc.dir/base/punc_base.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base/punc_base.c [ 60%] Linking C shared library libpunc.so cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/punc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libpunc.so.1.9 -o libpunc.so.1.9.3 CMakeFiles/punc.dir/base/punc_base.c.o -lmaloc /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so vf2c/libvf2c.so.1.9.3 cgcode/libcgcode.so.1.9.3 cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cmake -E cmake_symlink_library libpunc.so.1.9.3 libpunc.so.1.9 libpunc.so make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 60%] Built target punc make -f _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build.make _deps/fetk-build/mc/src/CMakeFiles/mc.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src/CMakeFiles/mc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build.make _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 60%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bmat.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bmat.c.o -MF CMakeFiles/mc.dir/bam/bmat.c.o.d -o CMakeFiles/mc.dir/bam/bmat.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c [ 60%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bvec.c.o [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/base/mc_base.c.o [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matln.c.o [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mat.c.o [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matcopy.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/base/mc_base.c.o -MF CMakeFiles/mc.dir/base/mc_base.c.o.d -o CMakeFiles/mc.dir/base/mc_base.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc_base.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o -MF CMakeFiles/mc.dir/bam/bsolv.c.o.d -o CMakeFiles/mc.dir/bam/bsolv.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bvec.c.o -MF CMakeFiles/mc.dir/bam/bvec.c.o.d -o CMakeFiles/mc.dir/bam/bvec.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mat.c.o -MF CMakeFiles/mc.dir/bam/mat.c.o.d -o CMakeFiles/mc.dir/bam/mat.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mat.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matcopy.c.o -MF CMakeFiles/mc.dir/bam/matcopy.c.o.d -o CMakeFiles/mc.dir/bam/matcopy.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/matcopy.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matln.c.o -MF CMakeFiles/mc.dir/bam/matln.c.o.d -o CMakeFiles/mc.dir/bam/matln.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/matln.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mtool.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mtool.c.o -MF CMakeFiles/mc.dir/bam/mtool.c.o.d -o CMakeFiles/mc.dir/bam/mtool.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mtool.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/slu.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/slu.c.o -MF CMakeFiles/mc.dir/bam/slu.c.o.d -o CMakeFiles/mc.dir/bam/slu.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/slu.c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c: In function ‘Bmat_ctor’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:36: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 104 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:32: note: directive argument in the range [0, 2147483646] 104 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:32: note: directive argument in the range [0, 3] In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bmat.h:121, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 4 and 22 bytes into a destination of size 15 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_bcg’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:922:29: warning: ‘%s’ directive writing up to 79 bytes into a region of size 72 [-Wformat-overflow=] 922 | sprintf(rn,"Bvec_bcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bvec.h:41, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 9 and 88 bytes into a destination of size 80 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:919:33: warning: ‘%s’ directive writing up to 79 bytes into a region of size 68 [-Wformat-overflow=] 919 | sprintf(rn,"--->Bvec_bcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bvec.h:41, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 13 and 92 bytes into a destination of size 80 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec.c.o -MF CMakeFiles/mc.dir/bam/vec.c.o.d -o CMakeFiles/mc.dir/bam/vec.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/vec.c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c: In function ‘Bmat_galerkin’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:36: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 1018 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:32: note: directive argument in the range [0, 2147483647] 1018 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:32: note: directive argument in the range [0, 2147483647] In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bmat.h:121, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 4 and 31 bytes into a destination of size 15 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cg’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:631:28: warning: ‘%s’ directive writing up to 79 bytes into a region of size 73 [-Wformat-overflow=] 631 | sprintf(rn,"Bvec_cg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bvec.h:41, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 8 and 87 bytes into a destination of size 80 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:628:32: warning: ‘%s’ directive writing up to 79 bytes into a region of size 69 [-Wformat-overflow=] 628 | sprintf(rn,"--->Bvec_cg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bvec.h:41, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 12 and 91 bytes into a destination of size 80 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec3.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec3.c.o -MF CMakeFiles/mc.dir/bam/vec3.c.o.d -o CMakeFiles/mc.dir/bam/vec3.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/vec3.c [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/zslu.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/zslu.c.o -MF CMakeFiles/mc.dir/bam/zslu.c.o.d -o CMakeFiles/mc.dir/bam/zslu.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/zslu.c [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/whb.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/whb.c.o -MF CMakeFiles/mc.dir/whb/whb.c.o.d -o CMakeFiles/mc.dir/whb/whb.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/whb.c [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/bvechb.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/bvechb.c.o -MF CMakeFiles/mc.dir/whb/bvechb.c.o.d -o CMakeFiles/mc.dir/whb/bvechb.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cgnr’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1422:30: warning: ‘%s’ directive writing up to 79 bytes into a region of size 71 [-Wformat-overflow=] 1422 | sprintf(rn,"Bvec_cgnr%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bvec.h:41, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 10 and 89 bytes into a destination of size 80 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1419:34: warning: ‘%s’ directive writing up to 79 bytes into a region of size 67 [-Wformat-overflow=] 1419 | sprintf(rn,"--->Bvec_cgnr%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bvec.h:41, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 14 and 93 bytes into a destination of size 80 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o -MF CMakeFiles/mc.dir/whb/hbtools.c.o.d -o CMakeFiles/mc.dir/whb/hbtools.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o -MF CMakeFiles/mc.dir/whb/rcmat.c.o.d -o CMakeFiles/mc.dir/whb/rcmat.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/rcmat.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/brcmat.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/brcmat.c.o -MF CMakeFiles/mc.dir/whb/brcmat.c.o.d -o CMakeFiles/mc.dir/whb/brcmat.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/brcmat.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/subopt.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/subopt.c.o -MF CMakeFiles/mc.dir/whb/subopt.c.o.d -o CMakeFiles/mc.dir/whb/subopt.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c: In function ‘Bvec_ctorPoint’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:28: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 291 | sprintf(bname, "%s_%d", thee->name, p); | ^~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:24: note: directive argument in the range [0, 2147483647] 291 | sprintf(bname, "%s_%d", thee->name, p); | ^~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 3 and 21 bytes into a destination of size 15 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/aprx.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/aprx.c.o -MF CMakeFiles/mc.dir/aprx/aprx.c.o.d -o CMakeFiles/mc.dir/aprx/aprx.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/aprx.c [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/assem.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/assem.c.o -MF CMakeFiles/mc.dir/aprx/assem.c.o.d -o CMakeFiles/mc.dir/aprx/assem.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/assem.c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hcg’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:267:29: warning: ‘%s’ directive writing up to 79 bytes into a region of size 72 [-Wformat-overflow=] 267 | sprintf(rn,"Bvec_hcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 9 and 88 bytes into a destination of size 80 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:264:33: warning: ‘%s’ directive writing up to 79 bytes into a region of size 68 [-Wformat-overflow=] 264 | sprintf(rn,"--->Bvec_hcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 13 and 92 bytes into a destination of size 80 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/bnode.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/bnode.c.o -MF CMakeFiles/mc.dir/aprx/bnode.c.o.d -o CMakeFiles/mc.dir/aprx/bnode.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/bnode.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/estim.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/estim.c.o -MF CMakeFiles/mc.dir/aprx/estim.c.o.d -o CMakeFiles/mc.dir/aprx/estim.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/estim.c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hbcg’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:474:30: warning: ‘%s’ directive writing up to 79 bytes into a region of size 71 [-Wformat-overflow=] 474 | sprintf(rn,"Bvec_hbcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 10 and 89 bytes into a destination of size 80 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:471:34: warning: ‘%s’ directive writing up to 79 bytes into a region of size 67 [-Wformat-overflow=] 471 | sprintf(rn,"--->Bvec_hbcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 14 and 93 bytes into a destination of size 80 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/eval.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/eval.c.o -MF CMakeFiles/mc.dir/aprx/eval.c.o.d -o CMakeFiles/mc.dir/aprx/eval.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/io.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/io.c.o -MF CMakeFiles/mc.dir/aprx/io.c.o.d -o CMakeFiles/mc.dir/aprx/io.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/io.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/node.c.o [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/parti.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/parti.c.o -MF CMakeFiles/mc.dir/aprx/parti.c.o.d -o CMakeFiles/mc.dir/aprx/parti.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/parti.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/node.c.o -MF CMakeFiles/mc.dir/aprx/node.c.o.d -o CMakeFiles/mc.dir/aprx/node.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/node.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/re.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/re.c.o -MF CMakeFiles/mc.dir/aprx/re.c.o.d -o CMakeFiles/mc.dir/aprx/re.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/re.c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:495:31: warning: ‘%s’ directive writing up to 79 bytes into a region of size 70 [-Wformat-overflow=] 495 | sprintf(rn,"Bvec_sfpcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:39: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 11 and 90 bytes into a destination of size 80 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:492:35: warning: ‘%s’ directive writing up to 79 bytes into a region of size 66 [-Wformat-overflow=] 492 | sprintf(rn,"--->Bvec_sfpcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:39: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 15 and 94 bytes into a destination of size 80 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:776:32: warning: ‘%s’ directive writing up to 79 bytes into a region of size 69 [-Wformat-overflow=] 776 | sprintf(rn,"Bvec_sfpbcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:39: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 12 and 91 bytes into a destination of size 80 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:773:36: warning: ‘%s’ directive writing up to 79 bytes into a region of size 65 [-Wformat-overflow=] 773 | sprintf(rn,"--->Bvec_sfpbcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:39: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 16 and 95 bytes into a destination of size 80 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function ‘Aprx_fe2fd’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:368:40: warning: ‘__builtin___sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 368 | sprintf(filename, "f%dz.dat", block); | ^ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/aprx_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 8 and 18 bytes into a destination of size 7 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:366:40: warning: ‘__builtin___sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 366 | sprintf(filename, "f%dy.dat", block); | ^ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/aprx_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 8 and 18 bytes into a destination of size 7 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:364:40: warning: ‘__builtin___sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 364 | sprintf(filename, "f%dx.dat", block); | ^ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/aprx_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 8 and 18 bytes into a destination of size 7 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/vel.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/vel.c.o -MF CMakeFiles/mc.dir/gem/vel.c.o.d -o CMakeFiles/mc.dir/gem/vel.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/vel.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/ves.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/ves.c.o -MF CMakeFiles/mc.dir/gem/ves.c.o.d -o CMakeFiles/mc.dir/gem/ves.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/ves.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gem.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gem.c.o -MF CMakeFiles/mc.dir/gem/gem.c.o.d -o CMakeFiles/mc.dir/gem/gem.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemchk.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemchk.c.o -MF CMakeFiles/mc.dir/gem/gemchk.c.o.d -o CMakeFiles/mc.dir/gem/gemchk.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemchk.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemdisp.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemdisp.c.o -MF CMakeFiles/mc.dir/gem/gemdisp.c.o.d -o CMakeFiles/mc.dir/gem/gemdisp.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemg.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemg.c.o -MF CMakeFiles/mc.dir/gem/gemg.c.o.d -o CMakeFiles/mc.dir/gem/gemg.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemg.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemgen.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemgen.c.o -MF CMakeFiles/mc.dir/gem/gemgen.c.o.d -o CMakeFiles/mc.dir/gem/gemgen.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemio.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemio.c.o -MF CMakeFiles/mc.dir/gem/gemio.c.o.d -o CMakeFiles/mc.dir/gem/gemio.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemio.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemref.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemref.c.o -MF CMakeFiles/mc.dir/gem/gemref.c.o.d -o CMakeFiles/mc.dir/gem/gemref.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemref.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemunref.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemunref.c.o -MF CMakeFiles/mc.dir/gem/gemunref.c.o.d -o CMakeFiles/mc.dir/gem/gemunref.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemunref.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemcube.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemcube.c.o -MF CMakeFiles/mc.dir/gem/gemcube.c.o.d -o CMakeFiles/mc.dir/gem/gemcube.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemcube.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/pde/pde.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/pde/pde.c.o -MF CMakeFiles/mc.dir/pde/pde.c.o.d -o CMakeFiles/mc.dir/pde/pde.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde/pde.c [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/am.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/am.c.o -MF CMakeFiles/mc.dir/nam/am.c.o.d -o CMakeFiles/mc.dir/nam/am.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/am.c [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/lsolv.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/lsolv.c.o -MF CMakeFiles/mc.dir/nam/lsolv.c.o.d -o CMakeFiles/mc.dir/nam/lsolv.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/lsolv.c [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/nsolv.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/nsolv.c.o -MF CMakeFiles/mc.dir/nam/nsolv.c.o.d -o CMakeFiles/mc.dir/nam/nsolv.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/nsolv.c [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/dyn.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/dyn.c.o -MF CMakeFiles/mc.dir/dyn/dyn.c.o.d -o CMakeFiles/mc.dir/dyn/dyn.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn/dyn.c [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/svio.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/svio.c.o -MF CMakeFiles/mc.dir/dyn/svio.c.o.d -o CMakeFiles/mc.dir/dyn/svio.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn/svio.c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function ‘Gem_writeTEC’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:33: warning: ‘__builtin___sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 1656 | sprintf(str1,"TETRAHEDRA"); | ^ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:41, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 11 bytes into a destination of size 10 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:33: warning: ‘TETRAHEDRON’ directive writing 11 bytes into a region of size 10 [-Wformat-overflow=] 1657 | sprintf(str2,"TETRAHEDRON"); | ~~~~~~~~~~^ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:41, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 12 bytes into a destination of size 10 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/mcsh/mcsh.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/mcsh/mcsh.c.o -MF CMakeFiles/mc.dir/mcsh/mcsh.c.o.d -o CMakeFiles/mc.dir/mcsh/mcsh.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c: In function ‘MCsh_builtIn’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: warning: ‘Gem_writeGEOM’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 765 | Gem_writeGEOM(thee->gm, | ^~~~~~~~~~~~~~~~~~~~~~~ 766 | sock, | ~~~~~ 767 | defKey, | ~~~~~~~ 768 | Vsh_getenvInt(thee->vsh,"CKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 769 | Vsh_getenvInt(thee->vsh,"DKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 770 | Vsh_getenvReal(thee->vsh,"GVAL"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 771 | Vsh_getenvInt(thee->vsh,"FKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 772 | defX, | ~~~~~ 773 | "GV"); | ~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: note: referencing argument 8 of type ‘double **’ In file included from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:42, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/mc/am.h:43, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/mc/nam.h:36, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mc/mcsh.h:42, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:34: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3036:15: note: in a call to function ‘Gem_writeGEOM’ 3036 | VEXTERNC void Gem_writeGEOM(Gem *thee, Vio *sock, | ^~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: warning: ‘Gem_writeGEOM’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 810 | Gem_writeGEOM(thee->gm, | ^~~~~~~~~~~~~~~~~~~~~~~ 811 | sock, | ~~~~~ 812 | defKey, | ~~~~~~~ 813 | Vsh_getenvInt(thee->vsh,"CKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 814 | Vsh_getenvInt(thee->vsh,"DKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 815 | Vsh_getenvReal(thee->vsh,"GVAL"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 816 | Vsh_getenvInt(thee->vsh,"FKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 817 | defX, | ~~~~~ 818 | "MATH"); | ~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: note: referencing argument 8 of type ‘double **’ In file included from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:42, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/mc/am.h:43, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/mc/nam.h:36, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mc/mcsh.h:42, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:34: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3036:15: note: in a call to function ‘Gem_writeGEOM’ 3036 | VEXTERNC void Gem_writeGEOM(Gem *thee, Vio *sock, | ^~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c: In function ‘Gem_delaunay’: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: warning: ‘Gem_writeGV’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 522 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: note: referencing argument 8 of type ‘double **’ In file included from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:34: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function ‘Gem_writeGV’ 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: warning: ‘Gem_writeGV’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 659 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: note: referencing argument 8 of type ‘double **’ In file included from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:34: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function ‘Gem_writeGV’ 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: warning: ‘Gem_writeGV’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 743 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: note: referencing argument 8 of type ‘double **’ In file included from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:34: /build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function ‘Gem_writeGV’ 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ [ 73%] Linking C shared library libmc.so cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/mc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libmc.so.1.9 -o libmc.so.1.9.3 CMakeFiles/mc.dir/base/mc_base.c.o CMakeFiles/mc.dir/bam/bmat.c.o CMakeFiles/mc.dir/bam/bsolv.c.o CMakeFiles/mc.dir/bam/bvec.c.o CMakeFiles/mc.dir/bam/mat.c.o CMakeFiles/mc.dir/bam/matcopy.c.o CMakeFiles/mc.dir/bam/matln.c.o CMakeFiles/mc.dir/bam/mtool.c.o CMakeFiles/mc.dir/bam/slu.c.o CMakeFiles/mc.dir/bam/vec.c.o CMakeFiles/mc.dir/bam/vec3.c.o CMakeFiles/mc.dir/bam/zslu.c.o CMakeFiles/mc.dir/whb/whb.c.o CMakeFiles/mc.dir/whb/bvechb.c.o CMakeFiles/mc.dir/whb/hbtools.c.o CMakeFiles/mc.dir/whb/rcmat.c.o CMakeFiles/mc.dir/whb/brcmat.c.o CMakeFiles/mc.dir/whb/subopt.c.o CMakeFiles/mc.dir/aprx/aprx.c.o CMakeFiles/mc.dir/aprx/assem.c.o CMakeFiles/mc.dir/aprx/bnode.c.o CMakeFiles/mc.dir/aprx/estim.c.o CMakeFiles/mc.dir/aprx/eval.c.o CMakeFiles/mc.dir/aprx/io.c.o CMakeFiles/mc.dir/aprx/node.c.o CMakeFiles/mc.dir/aprx/parti.c.o CMakeFiles/mc.dir/aprx/re.c.o CMakeFiles/mc.dir/gem/vel.c.o CMakeFiles/mc.dir/gem/ves.c.o CMakeFiles/mc.dir/gem/gem.c.o CMakeFiles/mc.dir/gem/gemchk.c.o CMakeFiles/mc.dir/gem/gemdisp.c.o CMakeFiles/mc.dir/gem/gemg.c.o CMakeFiles/mc.dir/gem/gemgen.c.o CMakeFiles/mc.dir/gem/gemio.c.o CMakeFiles/mc.dir/gem/gemref.c.o CMakeFiles/mc.dir/gem/gemunref.c.o CMakeFiles/mc.dir/gem/gemcube.c.o CMakeFiles/mc.dir/pde/pde.c.o CMakeFiles/mc.dir/nam/am.c.o CMakeFiles/mc.dir/nam/lsolv.c.o CMakeFiles/mc.dir/nam/nsolv.c.o CMakeFiles/mc.dir/dyn/dyn.c.o CMakeFiles/mc.dir/dyn/svio.c.o CMakeFiles/mc.dir/mcsh/mcsh.c.o /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so -lmaloc ../../punc/src/libpunc.so.1.9.3 /usr/lib/x86_64-linux-gnu/libblas.so -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../punc/src/vf2c/libvf2c.so.1.9.3 ../../punc/src/cgcode/libcgcode.so.1.9.3 cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cmake -E cmake_symlink_library libmc.so.1.9.3 libmc.so.1.9 libmc.so make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 73%] Built target mc make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/depend make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/src/generic /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc/CMakeFiles/apbs_pmgc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 73%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o -MF CMakeFiles/apbs_generic.dir/femparm.c.o.d -o CMakeFiles/apbs_generic.dir/femparm.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/femparm.c [ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o -MF CMakeFiles/apbs_generic.dir/nosh.c.o.d -o CMakeFiles/apbs_generic.dir/nosh.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/nosh.c [ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o [ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o [ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o -MF CMakeFiles/apbs_generic.dir/mgparm.c.o.d -o CMakeFiles/apbs_generic.dir/mgparm.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/mgparm.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o -MF CMakeFiles/apbs_generic.dir/bemparm.c.o.d -o CMakeFiles/apbs_generic.dir/bemparm.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/bemparm.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o -MF CMakeFiles/apbs_generic.dir/pbsamparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbsamparm.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/pbsamparm.c [ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o -MF CMakeFiles/apbs_generic.dir/pbamparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbamparm.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/pbamparm.c [ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o -MF CMakeFiles/apbs_generic.dir/pbeparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbeparm.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/pbeparm.c [ 76%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o -MF CMakeFiles/apbs_generic.dir/geoflowparm.c.o.d -o CMakeFiles/apbs_generic.dir/geoflowparm.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/geoflowparm.c [ 77%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildAd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildAd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/buildAd.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o -MF CMakeFiles/apbs_generic.dir/apolparm.c.o.d -o CMakeFiles/apbs_generic.dir/apolparm.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/apolparm.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o -MF CMakeFiles/apbs_generic.dir/vacc.c.o.d -o CMakeFiles/apbs_generic.dir/vacc.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/vacc.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/valist.c.o -MF CMakeFiles/apbs_generic.dir/valist.c.o.d -o CMakeFiles/apbs_generic.dir/valist.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/valist.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o -MF CMakeFiles/apbs_generic.dir/vatom.c.o.d -o CMakeFiles/apbs_generic.dir/vatom.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/vatom.c [ 78%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildBd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildBd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/buildBd.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o -MF CMakeFiles/apbs_generic.dir/vpbe.c.o.d -o CMakeFiles/apbs_generic.dir/vpbe.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/vpbe.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o -MF CMakeFiles/apbs_generic.dir/vcap.c.o.d -o CMakeFiles/apbs_generic.dir/vcap.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/vcap.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o -MF CMakeFiles/apbs_generic.dir/vclist.c.o.d -o CMakeFiles/apbs_generic.dir/vclist.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/vclist.c [ 79%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o -MF CMakeFiles/apbs_generic.dir/vstring.c.o.d -o CMakeFiles/apbs_generic.dir/vstring.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/vstring.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildGd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildGd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/buildGd.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o -MF CMakeFiles/apbs_generic.dir/vparam.c.o.d -o CMakeFiles/apbs_generic.dir/vparam.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/vparam.c [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildPd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildPd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/buildPd.c [ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o -MF CMakeFiles/apbs_generic.dir/vgreen.c.o.d -o CMakeFiles/apbs_generic.dir/vgreen.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/generic/vgreen.c [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o -MF CMakeFiles/apbs_pmgc.dir/matvecd.c.o.d -o CMakeFiles/apbs_pmgc.dir/matvecd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/matvecd.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o -MF CMakeFiles/apbs_pmgc.dir/cgd.c.o.d -o CMakeFiles/apbs_pmgc.dir/cgd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/cgd.c [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o -MF CMakeFiles/apbs_pmgc.dir/gsd.c.o.d -o CMakeFiles/apbs_pmgc.dir/gsd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/gsd.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgcsd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/mgcsd.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/mgdrvd.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgsubd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/mgsubd.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -MF CMakeFiles/apbs_pmgc.dir/mikpckd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/mikpckd.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -MF CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/mlinpckd.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o [ 83%] Linking C shared library libapbs_generic.so cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o -MF CMakeFiles/apbs_pmgc.dir/mypdec.c.o.d -o CMakeFiles/apbs_pmgc.dir/mypdec.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/mypdec.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_generic.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_generic.so.3 -o libapbs_generic.so.3 CMakeFiles/apbs_generic.dir/nosh.c.o CMakeFiles/apbs_generic.dir/mgparm.c.o CMakeFiles/apbs_generic.dir/femparm.c.o CMakeFiles/apbs_generic.dir/pbamparm.c.o CMakeFiles/apbs_generic.dir/pbsamparm.c.o CMakeFiles/apbs_generic.dir/pbeparm.c.o CMakeFiles/apbs_generic.dir/bemparm.c.o CMakeFiles/apbs_generic.dir/geoflowparm.c.o CMakeFiles/apbs_generic.dir/apolparm.c.o CMakeFiles/apbs_generic.dir/vacc.c.o CMakeFiles/apbs_generic.dir/valist.c.o CMakeFiles/apbs_generic.dir/vatom.c.o CMakeFiles/apbs_generic.dir/vpbe.c.o CMakeFiles/apbs_generic.dir/vcap.c.o CMakeFiles/apbs_generic.dir/vclist.c.o CMakeFiles/apbs_generic.dir/vstring.c.o CMakeFiles/apbs_generic.dir/vparam.c.o CMakeFiles/apbs_generic.dir/vgreen.c.o ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 -lutil -ldl -lm -lstdc++ -lpthread /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 /usr/lib/x86_64-linux-gnu/libblas.so [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o -MF CMakeFiles/apbs_pmgc.dir/newtond.c.o.d -o CMakeFiles/apbs_pmgc.dir/newtond.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/newtond.c [ 84%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -MF CMakeFiles/apbs_pmgc.dir/newdrvd.c.o.d -o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/newdrvd.c [ 84%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o -MF CMakeFiles/apbs_pmgc.dir/powerd.c.o.d -o CMakeFiles/apbs_pmgc.dir/powerd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/powerd.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cmake -E cmake_symlink_library libapbs_generic.so.3 libapbs_generic.so.3 libapbs_generic.so make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 84%] Built target apbs_generic [ 84%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o -MF CMakeFiles/apbs_pmgc.dir/smoothd.c.o.d -o CMakeFiles/apbs_pmgc.dir/smoothd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/smoothd.c [ 84%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgfasd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/pmgc/mgfasd.c make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/src/fem /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/fem /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/fem/CMakeFiles/apbs_fem.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 84%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o -MF CMakeFiles/apbs_fem.dir/vcsm.c.o.d -o CMakeFiles/apbs_fem.dir/vcsm.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vcsm.c [ 85%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vfetk.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vfetk.c.o -MF CMakeFiles/apbs_fem.dir/vfetk.c.o.d -o CMakeFiles/apbs_fem.dir/vfetk.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.c [ 85%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vpee.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vpee.c.o -MF CMakeFiles/apbs_fem.dir/vpee.c.o.d -o CMakeFiles/apbs_fem.dir/vpee.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vpee.c /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.c: In function ‘Vfetk_PDE_ctor2’: /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.c:1211:24: warning: assignment to ‘void (*)(struct sPDE *, int, int, double *, double *, double (*)[3])’ from incompatible pointer type ‘void (*)(PDE *, int, int, double *, double *)’ {aka ‘void (*)(struct sPDE *, int, int, double *, double *)’} [-Wincompatible-pointer-types] 1211 | thee->u_T = Vfetk_PDE_u_T; | ^ /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.c: In function ‘Bmat_printHB’: /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.c:1073:28: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1073 | sprintf(ptrfmt,"(%dI%d)",nptrline,numZdigits+1); | ^ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.h:67, from /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.c:57: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 6 and 18 bytes into a destination of size 17 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.c:1074:26: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 1074 | sprintf(ptrfmtstr,"%%%dd",numZdigits+1); | ^~ /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.c:1074:23: note: directive argument in the range [-2147483646, 2147483647] 1074 | sprintf(ptrfmtstr,"%%%dd",numZdigits+1); | ^~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.h:67, from /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.c:57: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 4 and 14 bytes into a destination of size 5 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.c:1075:28: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1075 | sprintf(indfmt,"(%dI%d)",nindline,nrowdigits+1); | ^ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.h:67, from /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.c:57: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 6 and 18 bytes into a destination of size 17 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.c:1076:26: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 1076 | sprintf(indfmtstr,"%%%dd",nrowdigits+1); | ^~ /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.c:1076:23: note: directive argument in the range [-2147483646, 2147483647] 1076 | sprintf(indfmtstr,"%%%dd",nrowdigits+1); | ^~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.h:67, from /build/apbs-A5U5s9/apbs-3.4.1/src/fem/vfetk.c:57: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 4 and 14 bytes into a destination of size 5 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 85%] Linking C shared library libapbs_fem.so cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/fem && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_fem.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_fem.so.3 -o libapbs_fem.so.3 CMakeFiles/apbs_fem.dir/vcsm.c.o CMakeFiles/apbs_fem.dir/vfetk.c.o CMakeFiles/apbs_fem.dir/vpee.c.o -lutil -ldl -lm -lstdc++ -lpthread /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/fem && /usr/bin/cmake -E cmake_symlink_library libapbs_fem.so.3 libapbs_fem.so.3 libapbs_fem.so make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 85%] Built target apbs_fem [ 85%] Linking CXX shared library libgamer.so cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gamer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgamer.so.1.9 -o libgamer.so.1.9.3 CMakeFiles/gamer.dir/base/gamer_base.c.o CMakeFiles/gamer.dir/triangle/triangle.c.o CMakeFiles/gamer.dir/tetgen/predicates.cpp.o CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o CMakeFiles/gamer.dir/biom/CorrectNormals.C.o CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o CMakeFiles/gamer.dir/biom/MarchingCube.C.o CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o CMakeFiles/gamer.dir/biom/PDB2Volume.C.o CMakeFiles/gamer.dir/biom/ReadLattice.C.o CMakeFiles/gamer.dir/biom/ReadPDB.C.o CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o CMakeFiles/gamer.dir/biom/RegionGrowing.C.o CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o CMakeFiles/gamer.dir/biom/SurfExtract.C.o CMakeFiles/gamer.dir/biom/SurfRefine.C.o CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -lmaloc cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cmake -E cmake_symlink_library libgamer.so.1.9.3 libgamer.so.1.9 libgamer.so make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 85%] Built target gamer [ 86%] Linking C shared library libapbs_pmgc.so cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pmgc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_pmgc.so.3 -o libapbs_pmgc.so.3 CMakeFiles/apbs_pmgc.dir/buildAd.c.o CMakeFiles/apbs_pmgc.dir/buildBd.c.o CMakeFiles/apbs_pmgc.dir/buildGd.c.o CMakeFiles/apbs_pmgc.dir/buildPd.c.o CMakeFiles/apbs_pmgc.dir/cgd.c.o CMakeFiles/apbs_pmgc.dir/gsd.c.o CMakeFiles/apbs_pmgc.dir/matvecd.c.o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o CMakeFiles/apbs_pmgc.dir/mypdec.c.o CMakeFiles/apbs_pmgc.dir/newtond.c.o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o CMakeFiles/apbs_pmgc.dir/powerd.c.o CMakeFiles/apbs_pmgc.dir/smoothd.c.o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 -lutil -ldl -lm -lstdc++ -lpthread /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 /usr/lib/x86_64-linux-gnu/libblas.so cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cmake -E cmake_symlink_library libapbs_pmgc.so.3 libapbs_pmgc.so.3 libapbs_pmgc.so make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 86%] Built target apbs_pmgc make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/src/mg /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o -MF CMakeFiles/apbs_mg.dir/vgrid.c.o.d -o CMakeFiles/apbs_mg.dir/vgrid.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/mg/vgrid.c [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o -MF CMakeFiles/apbs_mg.dir/vmgrid.c.o.d -o CMakeFiles/apbs_mg.dir/vmgrid.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/mg/vmgrid.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o -MF CMakeFiles/apbs_mg.dir/vopot.c.o.d -o CMakeFiles/apbs_mg.dir/vopot.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/mg/vopot.c [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o -MF CMakeFiles/apbs_mg.dir/vpmgp.c.o.d -o CMakeFiles/apbs_mg.dir/vpmgp.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/mg/vpmgp.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o -MF CMakeFiles/apbs_mg.dir/vpmg.c.o.d -o CMakeFiles/apbs_mg.dir/vpmg.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/mg/vpmg.c /build/apbs-A5U5s9/apbs-3.4.1/src/mg/vgrid.c: In function ‘Vgrid_readDXBIN’: /build/apbs-A5U5s9/apbs-3.4.1/src/mg/vgrid.c:853:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 853 | fgets(tok, VMAX_BUFSIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Linking C shared library libapbs_mg.so cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_mg.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_mg.so.3 -o libapbs_mg.so.3 CMakeFiles/apbs_mg.dir/vgrid.c.o CMakeFiles/apbs_mg.dir/vmgrid.c.o CMakeFiles/apbs_mg.dir/vopot.c.o CMakeFiles/apbs_mg.dir/vpmg.c.o CMakeFiles/apbs_mg.dir/vpmgp.c.o -lutil -ldl -lm -lstdc++ -lpthread /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../generic/libapbs_generic.so.3 ../pmgc/libapbs_pmgc.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg && /usr/bin/cmake -E cmake_symlink_library libapbs_mg.so.3 libapbs_mg.so.3 libapbs_mg.so make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 87%] Built target apbs_mg make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/src /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 87%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cc -Dapbs_routines_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/CMakeFiles/apbs_routines.dir/routines.c.o -MF CMakeFiles/apbs_routines.dir/routines.c.o.d -o CMakeFiles/apbs_routines.dir/routines.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c: In function ‘writematMG’: /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:2020:30: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2020 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/src/apbs.h:67, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.h:64, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c: In function ‘writedataMG’: /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:2919:34: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2919 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/src/apbs.h:67, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.h:64, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:2963:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2963 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/src/apbs.h:67, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.h:64, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:2954:34: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2954 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/src/apbs.h:67, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.h:64, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:2937:34: warning: ‘%s’ directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2937 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/src/apbs.h:67, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.h:64, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 6 and 1029 bytes into a destination of size 1024 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:2930:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2930 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/src/apbs.h:67, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.h:64, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:2944:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2944 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/src/apbs.h:67, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.h:64, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:2909:34: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2909 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/src/apbs.h:67, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.h:64, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 4 and 1027 bytes into a destination of size 1024 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c: In function ‘writedataFE’: /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:4887:34: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4887 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/src/apbs.h:67, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.h:64, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:4893:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4893 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/src/apbs.h:67, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.h:64, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:4880:34: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4880 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-A5U5s9/apbs-3.4.1/src/apbs.h:67, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.h:64, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 4 and 1027 bytes into a destination of size 1024 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c: In function ‘initAPOL’: /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:5046:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 5046 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:5046:20: note: referencing argument 2 of type ‘char *’ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:5046:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:5046:20: note: referencing argument 3 of type ‘char *’ In file included from /build/apbs-A5U5s9/apbs-3.4.1/src/generic/apolparm.h:73, from /build/apbs-A5U5s9/apbs-3.4.1/src/generic/nosh.h:73, from /build/apbs-A5U5s9/apbs-3.4.1/src/apbs.h:70, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.h:64, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:54: /build/apbs-A5U5s9/apbs-3.4.1/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:5048:24: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 5048 | atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:5048:24: note: referencing argument 2 of type ‘char *’ /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:5048:24: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:5048:24: note: referencing argument 3 of type ‘char *’ In file included from /build/apbs-A5U5s9/apbs-3.4.1/src/generic/apolparm.h:73, from /build/apbs-A5U5s9/apbs-3.4.1/src/generic/nosh.h:73, from /build/apbs-A5U5s9/apbs-3.4.1/src/apbs.h:70, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.h:64, from /build/apbs-A5U5s9/apbs-3.4.1/src/routines.c:54: /build/apbs-A5U5s9/apbs-3.4.1/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ [ 88%] Linking C shared library libapbs_routines.so cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_routines.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_routines.so.3 -o libapbs_routines.so.3 CMakeFiles/apbs_routines.dir/routines.c.o -lutil -ldl -lm -lstdc++ -lpthread /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp -lutil -ldl -lm -lstdc++ -lpthread /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp mg/libapbs_mg.so.3 fem/libapbs_fem.so.3 pmgc/libapbs_pmgc.so.3 generic/libapbs_generic.so.3 ../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library libapbs_routines.so.3 libapbs_routines.so.3 libapbs_routines.so make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 88%] Built target apbs_routines make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/depend make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/depend make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/depend make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/depend make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/src /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src/CMakeFiles/apbs.dir/DependInfo.cmake --color= make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/depend make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/mgmesh.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/smooth.dir/DependInfo.cmake --color= make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/depend cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/dxmath.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/mergedx.dir/DependInfo.cmake --color= make -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/mergedx2.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/value.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/multivalue.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/benchmark.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/similarity.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/build make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/build make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/build make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/build make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/build make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/build make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/build make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 88%] Building C object src/CMakeFiles/apbs.dir/main.c.o [ 89%] Building C object tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o [ 89%] Building C object tools/mesh/CMakeFiles/smooth.dir/smooth.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIE -fopenmp -MD -MT src/CMakeFiles/apbs.dir/main.c.o -MF CMakeFiles/apbs.dir/main.c.o.d -o CMakeFiles/apbs.dir/main.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/src/main.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o -MF CMakeFiles/mgmesh.dir/mgmesh.c.o.d -o CMakeFiles/mgmesh.dir/mgmesh.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/mgmesh.c [ 89%] Building C object tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/smooth.dir/smooth.c.o -MF CMakeFiles/smooth.dir/smooth.c.o.d -o CMakeFiles/smooth.dir/smooth.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/smooth.c [ 89%] Building C object tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o [ 89%] Building C object tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o -MF CMakeFiles/benchmark.dir/benchmark.c.o.d -o CMakeFiles/benchmark.dir/benchmark.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/benchmark.c make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/build cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o -MF CMakeFiles/dxmath.dir/dxmath.c.o.d -o CMakeFiles/dxmath.dir/dxmath.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/dxmath.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o -MF CMakeFiles/mergedx2.dir/mergedx2.c.o.d -o CMakeFiles/mergedx2.dir/mergedx2.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/mergedx2.c make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 89%] Building C object tools/mesh/CMakeFiles/similarity.dir/similarity.c.o [ 90%] Building C object tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/similarity.dir/similarity.c.o -MF CMakeFiles/similarity.dir/similarity.c.o.d -o CMakeFiles/similarity.dir/similarity.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/similarity.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o -MF CMakeFiles/mergedx.dir/mergedx.c.o.d -o CMakeFiles/mergedx.dir/mergedx.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/mergedx.c [ 91%] Building C object tools/mesh/CMakeFiles/value.dir/value.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/value.dir/value.c.o -MF CMakeFiles/value.dir/value.c.o.d -o CMakeFiles/value.dir/value.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/value.c [ 91%] Building C object tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o -MF CMakeFiles/multivalue.dir/multivalue.c.o.d -o CMakeFiles/multivalue.dir/multivalue.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/multivalue.c /build/apbs-A5U5s9/apbs-3.4.1/src/main.c: In function ‘main’: /build/apbs-A5U5s9/apbs-3.4.1/src/main.c:319:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 319 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/src/main.c:319:74: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 319 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ [ 91%] Linking C executable ../bin/mgmesh cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mgmesh.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mgmesh.dir/mgmesh.c.o -o ../bin/mgmesh ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 92%] Linking C executable ../bin/benchmark cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 [ 92%] Linking C executable ../bin/value cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/value.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/benchmark.dir/benchmark.c.o -o ../bin/benchmark ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/value.dir/value.c.o -o ../bin/value ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 93%] Linking C executable ../bin/multivalue cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/multivalue.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/multivalue.dir/multivalue.c.o -o ../bin/multivalue ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 93%] Linking C executable ../bin/smooth cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/smooth.dir/link.txt --verbose=1 [ 93%] Linking C executable ../bin/dxmath cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dxmath.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/smooth.dir/smooth.c.o -o ../bin/smooth ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dxmath.dir/dxmath.c.o -o ../bin/dxmath ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 93%] Linking C executable apbs cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/apbs.dir/main.c.o -o apbs -lutil -ldl -lm -lstdc++ -lpthread /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp libapbs_routines.so.3 mg/libapbs_mg.so.3 pmgc/libapbs_pmgc.so.3 fem/libapbs_fem.so.3 generic/libapbs_generic.so.3 ../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 94%] Linking C executable ../bin/similarity cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/similarity.dir/link.txt --verbose=1 [ 94%] Built target mgmesh make -f tools/mesh/CMakeFiles/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/analysis.dir/DependInfo.cmake --color= /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/similarity.dir/similarity.c.o -o ../bin/similarity ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 94%] Building C object tools/mesh/CMakeFiles/analysis.dir/analysis.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/analysis.dir/analysis.c.o -MF CMakeFiles/analysis.dir/analysis.c.o.d -o CMakeFiles/analysis.dir/analysis.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/analysis.c [ 94%] Built target benchmark make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/dx2mol.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 94%] Built target value make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/dx2uhbd.dir/DependInfo.cmake --color= [ 94%] Linking C executable ../bin/mergedx cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx.dir/link.txt --verbose=1 [ 94%] Building C object tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o -MF CMakeFiles/dx2mol.dir/dx2mol.c.o.d -o CMakeFiles/dx2mol.dir/dx2mol.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/dx2mol.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mergedx.dir/mergedx.c.o -o ../bin/mergedx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 94%] Building C object tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -MF CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o.d -o CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/dx2uhbd.c [ 94%] Built target smooth make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/del2dx.dir/DependInfo.cmake --color= [ 94%] Linking C executable ../bin/mergedx2 [ 94%] Built target dxmath cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx2.dir/link.txt --verbose=1 make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/tensor2dx.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/build /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mergedx2.dir/mergedx2.c.o -o ../bin/mergedx2 ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 94%] Built target multivalue make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/depend make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/uhbd_asc2bin.dir/DependInfo.cmake --color= [ 94%] Building C object tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o -MF CMakeFiles/del2dx.dir/del2dx.c.o.d -o CMakeFiles/del2dx.dir/del2dx.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/del2dx.c [ 94%] Built target apbs make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/manip /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/manip /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/manip/CMakeFiles/coulomb.dir/DependInfo.cmake --color= [ 95%] Building C object tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o -MF CMakeFiles/tensor2dx.dir/tensor2dx.c.o.d -o CMakeFiles/tensor2dx.dir/tensor2dx.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/tensor2dx.c make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 96%] Building C object tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o [ 96%] Building C object tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/manip && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o -MF CMakeFiles/coulomb.dir/coulomb.c.o.d -o CMakeFiles/coulomb.dir/coulomb.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/manip/coulomb.c cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -MF CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o.d -o CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c [ 96%] Built target similarity make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/manip /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/manip /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/manip/CMakeFiles/born.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 97%] Linking C executable ../bin/analysis cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysis.dir/link.txt --verbose=1 [ 97%] Built target mergedx make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/python /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/DependInfo.cmake --color= [ 97%] Building C object tools/manip/CMakeFiles/born.dir/born.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/manip && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/manip/CMakeFiles/born.dir/born.c.o -MF CMakeFiles/born.dir/born.c.o.d -o CMakeFiles/born.dir/born.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/manip/born.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/analysis.dir/analysis.c.o -o ../bin/analysis ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 98%] Linking C executable ../bin/dx2uhbd cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2uhbd.dir/link.txt --verbose=1 [ 98%] Building C object tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python && /usr/bin/cc -D_apbslib_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/python3.10 -I/build/apbs-A5U5s9/apbs-3.4.1/tools/python -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -MF CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o.d -o CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -c /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -o ../bin/dx2uhbd ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 98%] Linking C executable ../bin/dx2mol cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2mol.dir/link.txt --verbose=1 /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c: In function ‘main’: /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:30:5: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 30 | scanf("%s", flnm); | ^~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:42:5: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 42 | scanf("%s", newfile); | ^~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:54:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 54 | fscanf(inFile, "%s", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:57:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | fscanf(inFile, "%lf", &scale); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:60:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | fscanf(inFile, "%lf", &dum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:63:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 63 | fscanf(inFile, "%d", &grdflg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:66:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | fscanf(inFile, "%d", &idum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:69:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:72:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | fscanf(inFile, "%d", &one); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:75:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 75 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:78:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:81:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:84:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 84 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:87:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | fscanf(inFile, "%lf", &h); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:90:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 90 | fscanf(inFile, "%lf", &ox); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:93:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 93 | fscanf(inFile, "%lf", &oy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:96:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | fscanf(inFile, "%lf", &oz); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:99:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | fscanf(inFile, "%lf", &dum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:102:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 102 | fscanf(inFile, "%lf", &dum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:105:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 105 | fscanf(inFile, "%lf", &dum5); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:108:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 108 | fscanf(inFile, "%lf", &dum6); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:111:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | fscanf(inFile, "%lf", &dum7); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:114:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 114 | fscanf(inFile, "%lf", &dum8); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:117:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 117 | fscanf(inFile, "%d", &idum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:120:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 120 | fscanf(inFile, "%d", &idum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:125:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 125 | fscanf(inFile, "%d", &kk); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:128:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 128 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:131:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:138:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | fscanf(inFile, "%lf", RAT3(grid, i, j, k)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/del2dx.c: In function ‘main’: /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/del2dx.c:76:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | fread(&igrid, 1, sizeof(int), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/del2dx.c:89:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | fread(buffer, 1, sizeof(char) * 10, pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/del2dx.c:97:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fread(data, tot_grid, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/del2dx.c:103:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 103 | fread(&scale, 1, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/del2dx.c:106:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 106 | fread(oldmid, 3, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dx2mol.dir/dx2mol.c.o -o ../bin/dx2mol ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/tensor2dx.c: In function ‘main’: /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/tensor2dx.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf(pfile1,"%lf %lf %lf",&origin_xyz[0],&origin_xyz[1],&origin_xyz[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/tensor2dx.c:98:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 98 | fscanf(pfile1,"%lf %lf %lf",&gspace[0],&gspace[1],&gspace[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/tensor2dx.c:137:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/tensor2dx.c:138:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/tensor2dx.c:139:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 139 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/tensor2dx.c:140:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 140 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/tensor2dx.c:155:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/tensor2dx.c:156:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 156 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/tensor2dx.c:157:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-A5U5s9/apbs-3.4.1/tools/mesh/tensor2dx.c:158:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 158 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 98%] Built target mergedx2 make -f tools/python-pybind/CMakeFiles/apbs_pybind.dir/build.make tools/python-pybind/CMakeFiles/apbs_pybind.dir/depend make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-A5U5s9/apbs-3.4.1 /build/apbs-A5U5s9/apbs-3.4.1/tools/python-pybind /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python-pybind /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python-pybind/CMakeFiles/apbs_pybind.dir/DependInfo.cmake --color= [ 98%] Linking C executable ../bin/uhbd_asc2bin cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/uhbd_asc2bin.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/python-pybind/CMakeFiles/apbs_pybind.dir/build.make tools/python-pybind/CMakeFiles/apbs_pybind.dir/build make[3]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -o ../bin/uhbd_asc2bin ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 98%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/module.cpp.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -std=gnu++17 -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/module.cpp.o -MF CMakeFiles/apbs_pybind.dir/module.cpp.o.d -o CMakeFiles/apbs_pybind.dir/module.cpp.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/python-pybind/module.cpp [ 98%] Linking C executable ../bin/coulomb cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/coulomb.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/coulomb.dir/coulomb.c.o -o ../bin/coulomb ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 99%] Linking C executable ../bin/del2dx cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/del2dx.dir/link.txt --verbose=1 [ 99%] Linking C executable ../bin/tensor2dx cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/tensor2dx.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/tensor2dx.dir/tensor2dx.c.o -o ../bin/tensor2dx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/del2dx.dir/del2dx.c.o -o ../bin/del2dx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 99%] Built target analysis make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [ 99%] Built target dx2uhbd [ 99%] Built target uhbd_asc2bin [ 99%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -std=gnu++17 -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/python-pybind/bind_nosh.cpp [100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -std=gnu++17 -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/python-pybind/bind_vatom.cpp make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-A5U5s9/apbs-3.4.1/src -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-A5U5s9/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-A5U5s9/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -std=gnu++17 -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -c /build/apbs-A5U5s9/apbs-3.4.1/tools/python-pybind/bind_valist.cpp [100%] Built target dx2mol make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [100%] Built target del2dx make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [100%] Linking C executable ../bin/born cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/born.dir/link.txt --verbose=1 [100%] Built target tensor2dx [100%] Built target coulomb /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/born.dir/born.c.o -o ../bin/born ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [100%] Built target born [100%] Linking C shared library _apbslib.so cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/_apbslib.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,_apbslib.so -o _apbslib.so CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -lutil -ldl -lm -lstdc++ -lpthread /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../src/libapbs_routines.so.3 /usr/lib/x86_64-linux-gnu/libpython3.10.so ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [100%] Built target _apbslib [100%] Linking CXX shared module apbs.cpython-310-x86_64-linux-gnu.so cd /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python-pybind && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pybind.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/apbs-A5U5s9/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -o apbs.cpython-310-x86_64-linux-gnu.so CMakeFiles/apbs_pybind.dir/module.cpp.o CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -lutil -ldl -lm -lstdc++ -lpthread /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lpthread -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' [100%] Built target apbs_pybind make[2]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_build-indep make[1]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1' PYTHONPATH=/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python sphinx-build -b html docs /build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu/docs/_build/html # HTML generator Running Sphinx v4.5.0 making output directory... done WARNING: html_static_path entry '_static' does not exist [autosummary] generating autosummary for: api/index.rst, background.rst, formats/apbs-xml-parm.rst, formats/flat-parm.rst, formats/harwell.rst, formats/index.rst, formats/mcsf.rst, formats/opendx.rst, formats/pdb.rst, formats/pqr.rst, ..., using/input/old/generic/sdens.rst, using/input/old/generic/srad.rst, using/input/old/generic/swin.rst, using/input/old/generic/temp.rst, using/input/old/index.rst, using/input/old/print.rst, using/input/old/read.rst, using/tests.rst, using/tools.rst, using/units.rst loading intersphinx inventory from https://docs.python.org/3/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) building [mo]: targets for 0 po files that are out of date building [html]: targets for 127 source files that are out of date updating environment: [new config] 127 added, 0 changed, 0 removed reading sources... [ 0%] api/index reading sources... [ 1%] background reading sources... [ 2%] formats/apbs-xml-parm reading sources... [ 3%] formats/flat-parm reading sources... [ 3%] formats/harwell reading sources... [ 4%] formats/index reading sources... [ 5%] formats/mcsf reading sources... [ 6%] formats/opendx reading sources... [ 7%] formats/pdb reading sources... [ 7%] formats/pqr reading sources... [ 8%] formats/uhbd reading sources... [ 9%] formats/xml-struct reading sources... [ 10%] getting/index reading sources... [ 11%] getting/source reading sources... [ 11%] help reading sources... [ 12%] index reading sources... [ 13%] reading reading sources... [ 14%] releases reading sources... [ 14%] supporting reading sources... [ 15%] todo reading sources... [ 16%] using/examples/binding-energies reading sources... [ 17%] using/examples/salt-linkage reading sources... [ 18%] using/examples/solvation-energies reading sources... [ 18%] using/examples/visualization-pymol reading sources... [ 19%] using/examples/visualization-unitymol reading sources... [ 20%] using/index reading sources... [ 21%] using/input/new/calculate/boundary_element reading sources... [ 22%] using/input/new/calculate/finite_difference reading sources... [ 22%] using/input/new/calculate/finite_element reading sources... [ 23%] using/input/new/calculate/index reading sources... [ 24%] using/input/new/calculate/nonpolar reading sources... [ 25%] using/input/new/index reading sources... [ 25%] using/input/new/process reading sources... [ 26%] using/input/new/process_api reading sources... [ 27%] using/input/new/read reading sources... [ 28%] using/input/old/apolar/dpos reading sources... [ 29%] using/input/old/apolar/gamma reading sources... [ 29%] using/input/old/apolar/index reading sources... [ 30%] using/input/old/apolar/press reading sources... [ 31%] using/input/old/apolar/srfm reading sources... [ 32%] using/input/old/elec/3dmap reading sources... [ 33%] using/input/old/elec/akeyPRE reading sources... [ 33%] using/input/old/elec/akeySOLVE reading sources... [ 34%] using/input/old/elec/async reading sources... [ 35%] using/input/old/elec/bcfl reading sources... [ 36%] using/input/old/elec/cgcent reading sources... [ 37%] using/input/old/elec/cglen reading sources... [ 37%] using/input/old/elec/chgm reading sources... [ 38%] using/input/old/elec/diff reading sources... [ 39%] using/input/old/elec/dime reading sources... [ 40%] using/input/old/elec/domainLength reading sources... [ 40%] using/input/old/elec/dx reading sources... [ 41%] using/input/old/elec/ekey reading sources... [ 42%] using/input/old/elec/etol reading sources... [ 43%] using/input/old/elec/exp reading sources... [ 44%] using/input/old/elec/fe-manual reading sources... [ 44%] using/input/old/elec/fgcent reading sources... [ 45%] using/input/old/elec/fglen reading sources... [ 46%] using/input/old/elec/gamma-geoflow reading sources... [ 47%] using/input/old/elec/gcent reading sources... [ 48%] using/input/old/elec/geoflow-auto reading sources... [ 48%] using/input/old/elec/glen reading sources... [ 49%] using/input/old/elec/grid2d reading sources... [ 50%] using/input/old/elec/gridpts reading sources... [ 51%] using/input/old/elec/imat reading sources... [ 51%] using/input/old/elec/index reading sources... [ 52%] using/input/old/elec/ion reading sources... [ 53%] using/input/old/elec/lpbe reading sources... [ 54%] using/input/old/elec/lrpbe reading sources... [ 55%] using/input/old/elec/mac reading sources... [ 55%] using/input/old/elec/maxsolve reading sources... [ 56%] using/input/old/elec/maxvert reading sources... [ 57%] using/input/old/elec/mesh reading sources... [ 58%] using/input/old/elec/mg-auto reading sources... [ 59%] using/input/old/elec/mg-dummy reading sources... [ 59%] using/input/old/elec/mg-manual reading sources... [ 60%] using/input/old/elec/mg-para reading sources... [ 61%] using/input/old/elec/nlev reading sources... [ 62%] using/input/old/elec/npbe reading sources... [ 62%] using/input/old/elec/nrpbe reading sources... [ 63%] using/input/old/elec/ntraj reading sources... [ 64%] using/input/old/elec/ofrac reading sources... [ 65%] using/input/old/elec/outdata reading sources... [ 66%] using/input/old/elec/pbam-auto reading sources... [ 66%] using/input/old/elec/pbc reading sources... [ 67%] using/input/old/elec/pbsam-auto reading sources... [ 68%] using/input/old/elec/pdie reading sources... [ 69%] using/input/old/elec/pdime reading sources... [ 70%] using/input/old/elec/press-geoflow reading sources... [ 70%] using/input/old/elec/pygbe reading sources... [ 71%] using/input/old/elec/randorient reading sources... [ 72%] using/input/old/elec/runname reading sources... [ 73%] using/input/old/elec/runtype reading sources... [ 74%] using/input/old/elec/salt reading sources... [ 74%] using/input/old/elec/sdie reading sources... [ 75%] using/input/old/elec/srfm reading sources... [ 76%] using/input/old/elec/surf reading sources... [ 77%] using/input/old/elec/tabi reading sources... [ 77%] using/input/old/elec/targetNum reading sources... [ 78%] using/input/old/elec/targetRes reading sources... [ 79%] using/input/old/elec/term reading sources... [ 80%] using/input/old/elec/termcombine reading sources... [ 81%] using/input/old/elec/tolsp reading sources... [ 81%] using/input/old/elec/tree_n0 reading sources... [ 82%] using/input/old/elec/tree_order reading sources... [ 83%] using/input/old/elec/units reading sources... [ 84%] using/input/old/elec/usemap reading sources... [ 85%] using/input/old/elec/usemesh reading sources... [ 85%] using/input/old/elec/vdwdisp reading sources... [ 86%] using/input/old/elec/write reading sources... [ 87%] using/input/old/elec/writemat reading sources... [ 88%] using/input/old/elec/xyz reading sources... [ 88%] using/input/old/generic/bconc reading sources... [ 89%] using/input/old/generic/calcenergy reading sources... [ 90%] using/input/old/generic/calcforce reading sources... [ 91%] using/input/old/generic/grid reading sources... [ 92%] using/input/old/generic/mol reading sources... [ 92%] using/input/old/generic/sdens reading sources... [ 93%] using/input/old/generic/srad reading sources... [ 94%] using/input/old/generic/swin reading sources... [ 95%] using/input/old/generic/temp reading sources... [ 96%] using/input/old/index reading sources... [ 96%] using/input/old/print reading sources... [ 97%] using/input/old/read reading sources... [ 98%] using/tests reading sources... [ 99%] using/tools reading sources... [100%] using/units /build/apbs-A5U5s9/apbs-3.4.1/docs/getting/index.rst:41: ERROR: Unexpected indentation. /build/apbs-A5U5s9/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "geometric flow". /build/apbs-A5U5s9/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "fetk". /build/apbs-A5U5s9/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "pbam/pbsam". /build/apbs-A5U5s9/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "tabi-pb". looking for now-outdated files... none found pickling environment... done checking consistency... /build/apbs-A5U5s9/apbs-3.4.1/docs/using/input/old/elec/pygbe.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 0%] api/index writing output... [ 1%] background writing output... [ 2%] formats/apbs-xml-parm writing output... [ 3%] formats/flat-parm writing output... [ 3%] formats/harwell writing output... [ 4%] formats/index writing output... [ 5%] formats/mcsf writing output... [ 6%] formats/opendx writing output... [ 7%] formats/pdb writing output... [ 7%] formats/pqr writing output... [ 8%] formats/uhbd writing output... [ 9%] formats/xml-struct writing output... [ 10%] getting/index writing output... [ 11%] getting/source writing output... [ 11%] help writing output... [ 12%] index writing output... [ 13%] reading writing output... [ 14%] releases writing output... [ 14%] supporting writing output... [ 15%] todo writing output... [ 16%] using/examples/binding-energies writing output... [ 17%] using/examples/salt-linkage writing output... [ 18%] using/examples/solvation-energies writing output... [ 18%] using/examples/visualization-pymol writing output... [ 19%] using/examples/visualization-unitymol writing output... [ 20%] using/index writing output... [ 21%] using/input/new/calculate/boundary_element writing output... [ 22%] using/input/new/calculate/finite_difference writing output... [ 22%] using/input/new/calculate/finite_element writing output... [ 23%] using/input/new/calculate/index writing output... [ 24%] using/input/new/calculate/nonpolar writing output... [ 25%] using/input/new/index writing output... [ 25%] using/input/new/process writing output... [ 26%] using/input/new/process_api writing output... [ 27%] using/input/new/read writing output... [ 28%] using/input/old/apolar/dpos writing output... [ 29%] using/input/old/apolar/gamma writing output... [ 29%] using/input/old/apolar/index writing output... [ 30%] using/input/old/apolar/press writing output... [ 31%] using/input/old/apolar/srfm writing output... [ 32%] using/input/old/elec/3dmap writing output... [ 33%] using/input/old/elec/akeyPRE writing output... [ 33%] using/input/old/elec/akeySOLVE writing output... [ 34%] using/input/old/elec/async writing output... [ 35%] using/input/old/elec/bcfl writing output... [ 36%] using/input/old/elec/cgcent writing output... [ 37%] using/input/old/elec/cglen writing output... [ 37%] using/input/old/elec/chgm writing output... [ 38%] using/input/old/elec/diff writing output... [ 39%] using/input/old/elec/dime writing output... [ 40%] using/input/old/elec/domainLength writing output... [ 40%] using/input/old/elec/dx writing output... [ 41%] using/input/old/elec/ekey writing output... [ 42%] using/input/old/elec/etol writing output... [ 43%] using/input/old/elec/exp writing output... [ 44%] using/input/old/elec/fe-manual writing output... [ 44%] using/input/old/elec/fgcent writing output... [ 45%] using/input/old/elec/fglen writing output... [ 46%] using/input/old/elec/gamma-geoflow writing output... [ 47%] using/input/old/elec/gcent writing output... [ 48%] using/input/old/elec/geoflow-auto writing output... [ 48%] using/input/old/elec/glen writing output... [ 49%] using/input/old/elec/grid2d writing output... [ 50%] using/input/old/elec/gridpts writing output... [ 51%] using/input/old/elec/imat writing output... [ 51%] using/input/old/elec/index writing output... [ 52%] using/input/old/elec/ion writing output... [ 53%] using/input/old/elec/lpbe writing output... [ 54%] using/input/old/elec/lrpbe writing output... [ 55%] using/input/old/elec/mac writing output... [ 55%] using/input/old/elec/maxsolve writing output... [ 56%] using/input/old/elec/maxvert writing output... [ 57%] using/input/old/elec/mesh writing output... [ 58%] using/input/old/elec/mg-auto writing output... [ 59%] using/input/old/elec/mg-dummy writing output... [ 59%] using/input/old/elec/mg-manual writing output... [ 60%] using/input/old/elec/mg-para writing output... [ 61%] using/input/old/elec/nlev writing output... [ 62%] using/input/old/elec/npbe writing output... [ 62%] using/input/old/elec/nrpbe writing output... [ 63%] using/input/old/elec/ntraj writing output... [ 64%] using/input/old/elec/ofrac writing output... [ 65%] using/input/old/elec/outdata writing output... [ 66%] using/input/old/elec/pbam-auto writing output... [ 66%] using/input/old/elec/pbc writing output... [ 67%] using/input/old/elec/pbsam-auto writing output... [ 68%] using/input/old/elec/pdie writing output... [ 69%] using/input/old/elec/pdime writing output... [ 70%] using/input/old/elec/press-geoflow writing output... [ 70%] using/input/old/elec/pygbe writing output... [ 71%] using/input/old/elec/randorient writing output... [ 72%] using/input/old/elec/runname writing output... [ 73%] using/input/old/elec/runtype writing output... [ 74%] using/input/old/elec/salt writing output... [ 74%] using/input/old/elec/sdie writing output... [ 75%] using/input/old/elec/srfm writing output... [ 76%] using/input/old/elec/surf writing output... [ 77%] using/input/old/elec/tabi writing output... [ 77%] using/input/old/elec/targetNum writing output... [ 78%] using/input/old/elec/targetRes writing output... [ 79%] using/input/old/elec/term writing output... [ 80%] using/input/old/elec/termcombine writing output... [ 81%] using/input/old/elec/tolsp writing output... [ 81%] using/input/old/elec/tree_n0 writing output... [ 82%] using/input/old/elec/tree_order writing output... [ 83%] using/input/old/elec/units writing output... [ 84%] using/input/old/elec/usemap writing output... [ 85%] using/input/old/elec/usemesh writing output... [ 85%] using/input/old/elec/vdwdisp writing output... [ 86%] using/input/old/elec/write writing output... [ 87%] using/input/old/elec/writemat writing output... [ 88%] using/input/old/elec/xyz writing output... [ 88%] using/input/old/generic/bconc writing output... [ 89%] using/input/old/generic/calcenergy writing output... [ 90%] using/input/old/generic/calcforce writing output... [ 91%] using/input/old/generic/grid writing output... [ 92%] using/input/old/generic/mol writing output... [ 92%] using/input/old/generic/sdens writing output... [ 93%] using/input/old/generic/srad writing output... [ 94%] using/input/old/generic/swin writing output... [ 95%] using/input/old/generic/temp writing output... [ 96%] using/input/old/index writing output... [ 96%] using/input/old/print writing output... [ 97%] using/input/old/read writing output... [ 98%] using/tests writing output... [ 99%] using/tools writing output... [100%] using/units generating indices... genindex py-modindex done highlighting module code... [ 12%] apbs.input_file highlighting module code... [ 25%] apbs.input_file.calculate highlighting module code... [ 37%] apbs.input_file.calculate.boundary_element highlighting module code... [ 50%] apbs.input_file.calculate.finite_difference highlighting module code... [ 62%] apbs.input_file.calculate.finite_element highlighting module code... [ 75%] apbs.input_file.calculate.generic highlighting module code... [ 87%] apbs.input_file.process highlighting module code... [100%] apbs.input_file.read writing additional pages... search done copying images... [ 10%] media/pb-schematic.png copying images... [ 20%] media/apbs_bind_eng.png copying images... [ 30%] media/rna-qdens-pymol.jpg copying images... [ 40%] media/rna-qdens-vmd.jpg copying images... [ 50%] media/apbs_sol_eng.png copying images... [ 60%] media/fas2-iso-pymol.png copying images... [ 70%] media/fas2-surf-pymol.png copying images... [ 80%] media/1fas_VR.png copying images... [ 90%] media/UI.png copying images... [100%] media/AChE.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 8 warnings. The HTML pages are in obj-x86_64-linux-gnu/docs/_build/html. make[1]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-indep dh binary-indep --with python3,sphinxdoc --buildsystem=cmake dh_testroot -i -O--buildsystem=cmake dh_prep -i -O--buildsystem=cmake dh_installdirs -i -O--buildsystem=cmake dh_auto_install -i -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j10 install DESTDIR=/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/apbs-A5U5s9/apbs-3.4.1 -B/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "RELWITHDEBINFO" -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindAMD.cmake -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindARPACK.cmake -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindLAPACK.cmake -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindSuiteSparse.cmake -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindSuperLU.cmake -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindUMFPACK.cmake -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/punc/punc.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/punc/punc_base.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/punc/punccf.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/punc/punc_base_p.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libpunc.so.1.9.3 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libpunc.so.1.9 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libpunc.so -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/punc/varpack.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/punc/vblas.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/punc/vcgcode.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/punc/vlapack.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/punc/vpmg.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/punc/vf2c.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libvf2c.so -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libcgcode.so -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/gamer/gamer.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/gamer/gamer_base.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/gamer/triangle.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/gamer/tetgen.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/gamer/biom.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libgamer.so.1.9.3 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libgamer.so.1.9 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libgamer.so -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/mc_base.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/mc.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/bam.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/bmat.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/bvec.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/mat.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/mtool.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/slu.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/vec.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/vec3.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/zslu.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/whb.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/aprx.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/bnode.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/node.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/re.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/gem.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/vel.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/ves.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/pde.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/am.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/nam.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/dyn.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mc/mcsh.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libmc.so.1.9.3 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libmc.so.1.9 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libmc.so -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_routines.so.3 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_routines.so -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/apbs/apbs.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/apbs/routines.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/nosh.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/mgparm.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/femparm.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/pbamparm.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/pbsamparm.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/pbeparm.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/bemparm.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/geoflowparm.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/apolparm.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/vacc.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/valist.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/vatom.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/vpbe.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/vcap.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/vclist.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/vstring.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/vparam.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/vgreen.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/vmatrix.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/vhal.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/generic/vunit.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_generic.so.3 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_generic.so -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/buildAd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/buildBd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/buildGd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/buildPd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/cgd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/gsd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/matvecd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/mgcsd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/mgdrvd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/mgsubd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/mikpckd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/mlinpckd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/mypdec.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/newtond.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/newdrvd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/powerd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/smoothd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/pmgc/mgfasd.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_pmgc.so.3 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_pmgc.so -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mg/vgrid.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mg/vmgrid.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mg/vopot.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mg/vpmg.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/mg/vpmgp.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_mg.so.3 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_mg.so -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/fem/vcsm.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/fem/vfetk.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/include/fem/vpee.h -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_fem.so.3 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_fem.so -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/apbs.cpython-310-x86_64-linux-gnu.so -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-complex.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-mol.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-smol.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/1d7h-min.qcd -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.inp -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.log -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.oldlog -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/dmso-min.qcd -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/pqr2qcd -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-min.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-complex.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-mol.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-smol.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/1d7i-min.qcd -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.inp -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.log -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/dss-min.qcd -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-min.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/dmso-min.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/dss-min.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/aheall-atom.charmm.dat -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.full.log -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.inp -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/prot3.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/prot4.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/single.inp -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/srsrf.dot -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-auto.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-auto.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/complex.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/mesh.m -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/mol1.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/mol2.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/2-methylbutane.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/alkanes.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/apbs-forces.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/butane.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/cyclohexane.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/cyclopentane.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/ethane.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/force.result -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/hexane.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/isobutane.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/methane.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/mol.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/neopentane.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/parm.dat -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/pentane.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/propane.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30_monomer1.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30_monomer2.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer1.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer2.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASH66.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASP66.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-noASH66.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-noASP66.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/ASH66.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/ASP66.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASH66.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASP66.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASH66.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASP66.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/ASH66.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/ASP66.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/1a63_NanoShaper_SES.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/1a63_NanoShaper_Skin.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/451c_order1.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/451c_order5.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1a63.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1ajj.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1bbl.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins/451c.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins/oneb.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins/twob.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins/twob2.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-apolar.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-forces.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-mol-auto.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-mol-fem-extmesh.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-mol-fem.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-mol-parallel.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-smol-auto.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-smol-fem.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-smol-parallel.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apolarforces -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/ion.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/mesh.m -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/parm.dat -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/pmf.dat -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/polarforces -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/1a63.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/1a63.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/gly.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/gly.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/glycerol.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/imidazole.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/imidazole_zap.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.err -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.inp -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.out -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf.inp -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf.log -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf1.qcd -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.err -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.qcd -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/srsrf.dot -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/acet.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-mol.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-smol.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/complex.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/hca.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/mesh.m -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy-TEMPLATE.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Apbs_solv-TEMPLATE.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-0.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-12.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-16.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-4.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-8.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Run_membrane-helix.sh -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/draw_membrane2.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/apolarforces -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/complex.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/parm.dat -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/polarforces -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/runme.sh -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/491.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/491.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.e2.log -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.inp -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.log -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel12.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel2.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel12.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel2.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/complex.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/small491.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/UHBD -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.dat.exam -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.inp.exam -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.out.orig.exam -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.pdb.exam -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/acetate.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/acetic-acid.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/apbs-mol.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/apbs-smol.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/proton.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc/achbp.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc/apbs-PDB.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc/apbs.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc/fas2.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc/mache.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc/param.dat -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/1a63.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/1a63.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/neg_1.xyz -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/neg_2.xyz -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/neg_3.xyz -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/neg_charge.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/pos_1.xyz -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/pos_2.xyz -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/pos_3.xyz -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/pos_charge.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/toy_dynamics.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/toy_electrostatic.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/toy_energyforce.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barn_bars_electro.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barnase.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barstar.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.vert -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg2.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_dynamics.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_electrostatic.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_energyforce.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_electrostatic.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_msms.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_1_1.xyz -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_1_2.xyz -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_2_1.xyz -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_2_2.xyz -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/README -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-apo.out -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-bin.out -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-lig.out -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-apo.out -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-bin.out -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-lig.out -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-surf.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-vdw.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-surf.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-vdw.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_apo_apbs.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_bin_apbs.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_lig_apbs.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/apbs.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_1.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_1.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_2.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_2.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_3.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_3.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_4.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_4.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/energy.dat -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/mol0.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/mol1.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/mol2.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/mol3.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/mol4.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/point-pmf-0.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/runme.sh -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/PDB -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outBoxB19.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outNB.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outNpep.pdb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath.txt -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/model_outBoxB19.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/model_outNB.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/model_outNpep.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/run_apdx_files.sh -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/template.txt -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/test.sh -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/fit.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/apbs_dx.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/postprocess.sh -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1.face -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1.vert -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_1.face -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_1.vert -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_2.face -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_2.vert -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_3.face -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_3.vert -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_stern.face -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_stern.vert -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys.config -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys.param -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys1_charges.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/run_examples.sh -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/run_selected_examples.sh -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/UHBD -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.dat.exam -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.inp.exam -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.out.orig.exam -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/apbs-mol.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/apbs-smol.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/methanol.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/methoxide.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tests -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tests/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tests/apbs_logger.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tests/apbs_check_forces.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tests/apbs_check_results.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tests/apbs_check_intermediate_energies.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tests/apbs_tester.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tests/test_cases.cfg -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/CMakeLists.txt -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/README.md -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/WHATIF2AMBER.sed -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/amber2charmm.sh -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/amber-param.dat -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/amber2uhbd.sh -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/weiner86-param.dat -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/c-alpha.dat -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/vparam -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/vparam/vparam-amber-parm94.dat -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/vparam/vparam-amber-parm94.xml -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/qcd2pqr.awk -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/github -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/github/getReleases.sh -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/github/release-data.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip/CMakeLists.txt -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip/born.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip/coulomb.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip/inputgen.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip/psize.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/CMakeLists.txt -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/analysis.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/benchmark.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/del2dx.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/dx2mol.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/dx2uhbd.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/dxmath.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/mergedx.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/mergedx2.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/mgmesh.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/multivalue.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/similarity.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/smooth.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/tensor2dx.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/uhbd_asc2bin.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/value.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/CMakeLists.txt -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_constants.hpp -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_nosh.cpp -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_nosh.hpp -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_valist.cpp -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_valist.hpp -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_vatom.cpp -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_vatom.hpp -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/module.cpp -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/Makefile -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/Makefile.am -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/Makefile.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/README -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/apbs.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/apbslib.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/apbslib.i -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/apbslib_wrap.doc -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/ion.pqr -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/main.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile.am -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile.in -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/README -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/average.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/mergedx.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/read.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/vgrid.i -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/vgrid.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/vgridlib.c -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/noinput.py -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/CMakeLists.txt -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.cfg -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.net -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cfg -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cm -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.net -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cfg -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cm -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.net -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.cfg -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.net -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/mgmesh -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/benchmark -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/value -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/multivalue -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/smooth -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/dxmath -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/similarity -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/mergedx -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/mergedx2 -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/analysis -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/dx2uhbd -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/dx2mol -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/uhbd_asc2bin -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/coulomb -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/tensor2dx -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/del2dx -- Installing: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/born make[1]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1' (cd tests; PATH=/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin:${PATH} LD_LIBRARY_PATH=/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu:${LD_LIBRARY_PATH} PYTHONPATH=${PYTHONPATH}:/build/apbs-A5U5s9/apbs-3.4.1/tools/manip python3 apbs_tester.py -c test_cases.cfg; rm -rf __pycache__) TESTING WITH BINARY_NAME:apbs START_DIR:/build/apbs-A5U5s9/apbs-3.4.1/build -------------------------------------------------------------------------------- Testing forces from apbs-forces.in Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.003229 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in CHECKING:/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs NOTE: Using apbs binary:/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs Testing all sections The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv ================================================================================ Running tests for born section BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.607073836227E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200266567971E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to potential.dx.gz Total electrostatic energy = 4.732245131587E+03 kJ/mol Calculating forces... Writing potential to potential-PE0.dx.gz ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.297735526282E+02 kJ/mol Global net ELEC energy = -2.297735526282E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) *** PASSED *** Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) *** PASSED *** Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) *** PASSED *** Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) *** PASSED *** Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) *** PASSED *** Elapsed time: 2.128561 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in Checking for intermediate energies in input file apbs-mol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] COMPUTED RESULT 960.7073836227 COMPUTED RESULT 2200.266567971 COMPUTED RESULT 4732.245131587 COMPUTED RESULT 1190.871482831 COMPUTED RESULT 2430.874049735 COMPUTED RESULT 4962.018684215 COMPUTED RESULT -229.7735526282 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.532928767450E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.201243880085E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.733006258977E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.290124252387E+02 kJ/mol Global net ELEC energy = -2.290124252387E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) *** PASSED *** Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) *** PASSED *** Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) *** PASSED *** Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) *** PASSED *** Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) *** PASSED *** Elapsed time: 2.5726430000000002 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Checking for intermediate energies in input file apbs-smol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] COMPUTED RESULT 953.292876745 COMPUTED RESULT 2201.243880085 COMPUTED RESULT 4733.006258977 COMPUTED RESULT 1190.871482831 COMPUTED RESULT 2430.874049735 COMPUTED RESULT 4962.018684215 COMPUTED RESULT -229.0124252387 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE0.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935592471E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255308186E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864094552E+01 kJ/mol Global net ELEC energy = -5.761864094552E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 0 results: 2.401768459022e+02 8.142935592471e+02 1.485255308186e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.761864094552e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE0.out BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE1.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778312125E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246667424E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728170718E+01 kJ/mol Global net ELEC energy = -5.762728170718E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 1 results: 2.401768459022e+02 8.142778312125e+02 1.485246667424e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.762728170718e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE1.out BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE2.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935605696E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255306569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864257239E+01 kJ/mol Global net ELEC energy = -5.761864257239E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 2 results: 2.401768459091e+02 8.142935605696e+02 1.485255306569e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.761864257239e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE2.out BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE3.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778325440E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246665692E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728344954E+01 kJ/mol Global net ELEC energy = -5.762728344954E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 3 results: 2.401768459091e+02 8.142778325440e+02 1.485246665692e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.762728344954e+01 Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) *** PASSED *** Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) *** PASSED *** Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) *** PASSED *** Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) *** PASSED *** Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) *** PASSED *** Elapsed time: 13.120709 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Checking for intermediate energies in input file apbs-mol-parallel-PE3.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [960.7073836226, 3257.1427835731997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867463003] EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] COMPUTED RESULT 960.7073836226 COMPUTED RESULT 3257.1427835731997 COMPUTED RESULT 5941.0039478710005 COMPUTED RESULT 1190.8714828309999 COMPUTED RESULT 3519.7218230368003 COMPUTED RESULT 6171.495796544 COMPUTED RESULT -230.49184867463003 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE0.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE0.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369591602E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524998001E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895113069E+01 kJ/mol Global net ELEC energy = -5.734895113069E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 0 results: 2.383232191816e+02 8.145369591602e+02 1.485524998001e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.734895113069e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE0.out BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE1.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419898332E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328612E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462051928E+01 kJ/mol Global net ELEC energy = -5.734462051928E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 1 results: 2.383232191816e+02 8.145419898332e+02 1.485529328612e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.734462051928e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE1.out BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE2.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369593489E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524997676E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895146550E+01 kJ/mol Global net ELEC energy = -5.734895146550E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 2 results: 2.383232191909e+02 8.145369593489e+02 1.485524997676e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.734895146550e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE2.out BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE3.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419900310E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328301E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462084052E+01 kJ/mol Global net ELEC energy = -5.734462084052E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 3 results: 2.383232191909e+02 8.145419900310e+02 1.485529328301e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.734462084052e+01 Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) *** PASSED *** Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) *** PASSED *** Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) *** PASSED *** Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) *** PASSED *** Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) *** PASSED *** Elapsed time: 12.677288 seconds -------------------------------------------------------------------------------- Total elapsed time: 30.50243 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in Checking for intermediate energies in input file apbs-smol-parallel-PE3.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] COMPUTED RESULT 953.292876745 COMPUTED RESULT 3258.1578983732998 COMPUTED RESULT 5942.108652589999 COMPUTED RESULT 1190.8714828309999 COMPUTED RESULT 3519.7218230368003 COMPUTED RESULT 6171.495796544 COMPUTED RESULT -229.38714395599 Running tests for actin-dimer-auto section BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527617850342E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.919510754196E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527671844880E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.915468859278E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.056317807611E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.836028296532E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.048683058625E+02 kJ/mol Global net ELEC energy = 1.048683058625E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) *** PASSED *** Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) *** PASSED *** Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) *** PASSED *** Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) *** PASSED *** Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) *** PASSED *** Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) *** PASSED *** Testing computed result against expected result (1.048683058625e+02, 1.048683060915e+02) *** PASSED *** Elapsed time: 123.710359 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in Checking for intermediate energies in input file apbs-mol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058625] EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] COMPUTED RESULT 152761.7850342 COMPUTED RESULT 291951.0754196 COMPUTED RESULT 152767.184488 COMPUTED RESULT 291546.8859278 COMPUTED RESULT 305631.7807611 COMPUTED RESULT 583602.8296532 COMPUTED RESULT 104.8683058625 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.528632421825E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.920618662320E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.529297900572E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.916592202835E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.059244262535E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.838306706232E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.095841077691E+02 kJ/mol Global net ELEC energy = 1.095841077691E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05) *** PASSED *** Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) *** PASSED *** Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) *** PASSED *** Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) *** PASSED *** Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) *** PASSED *** Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) *** PASSED *** Testing computed result against expected result (1.095841077691e+02, 1.095841074454e+02) *** PASSED *** Elapsed time: 73.370461 seconds -------------------------------------------------------------------------------- Total elapsed time: 197.08082 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file alkanes.in Checking for intermediate energies in input file apbs-smol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077691] EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] COMPUTED RESULT 152863.2421825 COMPUTED RESULT 292061.866232 COMPUTED RESULT 152929.7900572 COMPUTED RESULT 291659.2202835 COMPUTED RESULT 305924.4262535 COMPUTED RESULT 583830.6706232 COMPUTED RESULT 109.5841077691 Running tests for alkanes section BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: alkanes.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'alkanes.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file alkanes.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 11 molecules Reading PDB-format atom data from 2-methylbutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 4.33e+00 e Reading PDB-format atom data from butane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (3.917e+00, 7.025e-01, -8.575e+00) Net charge 3.51e+00 e Reading PDB-format atom data from cyclohexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (1.123e+00, 5.880e-01, 7.680e-01) Net charge 4.93e+00 e Reading PDB-format atom data from cyclopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 13 atoms Centered at (1.320e+00, 5.255e-01, 1.289e+00) Net charge 3.88e+00 e Reading PDB-format atom data from ethane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (2.210e-01, -2.100e-02, 7.650e-01) Net charge 1.87e+00 e Reading PDB-format atom data from hexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 20 atoms Centered at (4.951e+00, -9.500e-03, -8.406e+00) Net charge 5.16e+00 e Reading PDB-format atom data from isobutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.859e+01, 1.864e+01, 1.921e+01) Net charge 3.51e+00 e Reading PDB-format atom data from methane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5 atoms Centered at (1.803e+01, 1.779e+01, 1.782e+01) Net charge 1.05e+00 e Reading PDB-format atom data from neopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (1.867e+01, 1.894e+01, 1.920e+01) Net charge 4.33e+00 e Reading PDB-format atom data from pentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (4.460e+00, 1.615e-01, -8.566e+00) Net charge 4.33e+00 e Reading PDB-format atom data from propane.pdb. 11 atoms Centered at (1.836e+01, 1.896e+01, 1.861e+01) Net charge 2.69e+00 e Preparing to run 11 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated-2-methylbutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.815624614267E+00 SASA for atom 1: 0.000000000000E+00 SASA for atom 2: 6.122920124655E-01 SASA for atom 3: 3.957497153740E+00 SASA for atom 4: 4.308445014544E+00 SASA for atom 5: 1.843264951960E+01 SASA for atom 6: 1.837011296483E+01 SASA for atom 7: 1.666599184724E+01 SASA for atom 8: 1.480031796315E+01 SASA for atom 9: 1.603020354037E+01 SASA for atom 10: 1.473778140838E+01 SASA for atom 11: 1.611879699297E+01 SASA for atom 12: 1.810954398660E+01 SASA for atom 13: 1.420100931324E+01 SASA for atom 14: 1.437298483886E+01 SASA for atom 15: 1.814081226399E+01 SASA for atom 16: 2.152820898091E+01 Total solvent accessible surface area: 214.202 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.243280922127E-02 Surface tension*area energy for atom 1: 0.000000000000E+00 Surface tension*area energy for atom 2: 5.204482105957E-03 Surface tension*area energy for atom 3: 3.363872580679E-02 Surface tension*area energy for atom 4: 3.662178262362E-02 Surface tension*area energy for atom 5: 1.566775209166E-01 Surface tension*area energy for atom 6: 1.561459602010E-01 Surface tension*area energy for atom 7: 1.416609307015E-01 Surface tension*area energy for atom 8: 1.258027026868E-01 Surface tension*area energy for atom 9: 1.362567300932E-01 Surface tension*area energy for atom 10: 1.252711419712E-01 Surface tension*area energy for atom 11: 1.370097744402E-01 Surface tension*area energy for atom 12: 1.539311238861E-01 Surface tension*area energy for atom 13: 1.207085791625E-01 Surface tension*area energy for atom 14: 1.221703711303E-01 Surface tension*area energy for atom 15: 1.541969042439E-01 Surface tension*area energy for atom 16: 1.829897763377E-01 Total surface tension energy: 1.82072 kJ/mol Total solvent accessible volume: 253.665 A^3 Total pressure*volume energy: 60.7274 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.271287875274E+00 WCA energy for atom 1: -5.600872869478E+00 WCA energy for atom 2: -5.773775123943E+00 WCA energy for atom 3: -6.072801488986E+00 WCA energy for atom 4: -6.378470721845E+00 WCA energy for atom 5: -1.573474558351E+00 WCA energy for atom 6: -1.582338715648E+00 WCA energy for atom 7: -1.504044838266E+00 WCA energy for atom 8: -1.351002262819E+00 WCA energy for atom 9: -1.437367175239E+00 WCA energy for atom 10: -1.384626257493E+00 WCA energy for atom 11: -1.468867560891E+00 WCA energy for atom 12: -1.557005662832E+00 WCA energy for atom 13: -1.473759654043E+00 WCA energy for atom 14: -1.502261431335E+00 WCA energy for atom 15: -1.550940901474E+00 WCA energy for atom 16: -1.667828659696E+00 Total WCA energy: -48.1507 kJ/mol Total non-polar energy = 1.439739455792E+01 kJ/mol ---------------------------------------- CALCULATION #2 (solvated-butane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 8.064333822716E-01 SASA for atom 3: 4.375647796400E+00 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.660345529247E+01 SASA for atom 8: 1.658782115377E+01 SASA for atom 9: 1.658260977421E+01 SASA for atom 10: 1.658260977421E+01 SASA for atom 11: 2.145003828744E+01 SASA for atom 12: 1.852124297220E+01 SASA for atom 13: 1.856293400871E+01 Total solvent accessible surface area: 193.855 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 6.854683749309E-03 Surface tension*area energy for atom 3: 3.719300626940E-02 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.411293699860E-01 Surface tension*area energy for atom 8: 1.409964798071E-01 Surface tension*area energy for atom 9: 1.409521830808E-01 Surface tension*area energy for atom 10: 1.409521830808E-01 Surface tension*area energy for atom 11: 1.823253254433E-01 Surface tension*area energy for atom 12: 1.574305652637E-01 Surface tension*area energy for atom 13: 1.577849390741E-01 Total surface tension energy: 1.64777 kJ/mol Total solvent accessible volume: 217.863 A^3 Total pressure*volume energy: 52.1564 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.728858147814E+00 WCA energy for atom 1: -6.204037472587E+00 WCA energy for atom 2: -6.202937735018E+00 WCA energy for atom 3: -6.728762249931E+00 WCA energy for atom 4: -1.623549989062E+00 WCA energy for atom 5: -1.709092300778E+00 WCA energy for atom 6: -1.625196457114E+00 WCA energy for atom 7: -1.484289341167E+00 WCA energy for atom 8: -1.485410538626E+00 WCA energy for atom 9: -1.485593139015E+00 WCA energy for atom 10: -1.484878734279E+00 WCA energy for atom 11: -1.708585062695E+00 WCA energy for atom 12: -1.625094916482E+00 WCA energy for atom 13: -1.624416805392E+00 Total WCA energy: -41.7207 kJ/mol Total non-polar energy = 1.208346456826E+01 kJ/mol ---------------------------------------- CALCULATION #3 (solvated-cyclohexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 7.840324549863E-01 SASA for atom 1: 8.064333822716E-01 SASA for atom 2: 8.288343095569E-01 SASA for atom 3: 7.840324549863E-01 SASA for atom 4: 7.989664065098E-01 SASA for atom 5: 8.363012853187E-01 SASA for atom 6: 2.001169752764E+01 SASA for atom 7: 1.616048802948E+01 SASA for atom 8: 2.001169752764E+01 SASA for atom 9: 1.619175630687E+01 SASA for atom 10: 1.616048802948E+01 SASA for atom 11: 1.993352683418E+01 SASA for atom 12: 2.001169752764E+01 SASA for atom 13: 1.618133354774E+01 SASA for atom 14: 1.617091078861E+01 SASA for atom 15: 2.001690890721E+01 SASA for atom 16: 1.993873821374E+01 SASA for atom 17: 1.617091078861E+01 Total solvent accessible surface area: 221.799 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 6.664275867383E-03 Surface tension*area energy for atom 1: 6.854683749309E-03 Surface tension*area energy for atom 2: 7.045091631234E-03 Surface tension*area energy for atom 3: 6.664275867383E-03 Surface tension*area energy for atom 4: 6.791214455333E-03 Surface tension*area energy for atom 5: 7.108560925209E-03 Surface tension*area energy for atom 6: 1.700994289850E-01 Surface tension*area energy for atom 7: 1.373641482506E-01 Surface tension*area energy for atom 8: 1.700994289850E-01 Surface tension*area energy for atom 9: 1.376299286084E-01 Surface tension*area energy for atom 10: 1.373641482506E-01 Surface tension*area energy for atom 11: 1.694349780905E-01 Surface tension*area energy for atom 12: 1.700994289850E-01 Surface tension*area energy for atom 13: 1.375413351558E-01 Surface tension*area energy for atom 14: 1.374527417032E-01 Surface tension*area energy for atom 15: 1.701437257113E-01 Surface tension*area energy for atom 16: 1.694792748168E-01 Surface tension*area energy for atom 17: 1.374527417032E-01 Total surface tension energy: 1.88529 kJ/mol Total solvent accessible volume: 267.435 A^3 Total pressure*volume energy: 64.0239 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -5.793234697241E+00 WCA energy for atom 1: -5.784370526583E+00 WCA energy for atom 2: -5.791799130412E+00 WCA energy for atom 3: -5.788504399087E+00 WCA energy for atom 4: -5.797319672490E+00 WCA energy for atom 5: -5.787358035342E+00 WCA energy for atom 6: -1.523887929614E+00 WCA energy for atom 7: -1.413678912317E+00 WCA energy for atom 8: -1.521751604392E+00 WCA energy for atom 9: -1.414741802525E+00 WCA energy for atom 10: -1.413367854344E+00 WCA energy for atom 11: -1.523407238081E+00 WCA energy for atom 12: -1.523000623583E+00 WCA energy for atom 13: -1.413922068538E+00 WCA energy for atom 14: -1.416316744211E+00 WCA energy for atom 15: -1.524577474659E+00 WCA energy for atom 16: -1.523300410052E+00 WCA energy for atom 17: -1.414522566061E+00 Total WCA energy: -52.3691 kJ/mol Total non-polar energy = 1.354016672221E+01 kJ/mol ---------------------------------------- CALCULATION #4 (solvated-cyclopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 9.490526193215E+00 SASA for atom 1: 9.512927120500E+00 SASA for atom 2: 2.299828534626E+00 SASA for atom 3: 1.919012770776E+00 SASA for atom 4: 2.307295510388E+00 SASA for atom 5: 2.325838699632E+01 SASA for atom 6: 2.325838699632E+01 SASA for atom 7: 2.045987617019E+01 SASA for atom 8: 2.067875411190E+01 SASA for atom 9: 2.028790064456E+01 SASA for atom 10: 1.897463299431E+01 SASA for atom 11: 2.048593306801E+01 SASA for atom 12: 2.070481100972E+01 Total solvent accessible surface area: 193.638 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.066947264233E-02 Surface tension*area energy for atom 1: 8.085988052425E-02 Surface tension*area energy for atom 2: 1.954854254432E-02 Surface tension*area energy for atom 3: 1.631160855160E-02 Surface tension*area energy for atom 4: 1.961201183830E-02 Surface tension*area energy for atom 5: 1.976962894687E-01 Surface tension*area energy for atom 6: 1.976962894687E-01 Surface tension*area energy for atom 7: 1.739089474466E-01 Surface tension*area energy for atom 8: 1.757694099511E-01 Surface tension*area energy for atom 9: 1.724471554788E-01 Surface tension*area energy for atom 10: 1.612843804516E-01 Surface tension*area energy for atom 11: 1.741304310781E-01 Surface tension*area energy for atom 12: 1.759908935826E-01 Total surface tension energy: 1.64593 kJ/mol Total solvent accessible volume: 217.998 A^3 Total pressure*volume energy: 52.1887 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.343496616804E+00 WCA energy for atom 1: -6.327869601807E+00 WCA energy for atom 2: -6.334858040579E+00 WCA energy for atom 3: -6.296075406417E+00 WCA energy for atom 4: -6.345600816761E+00 WCA energy for atom 5: -1.663697465126E+00 WCA energy for atom 6: -1.662444032853E+00 WCA energy for atom 7: -1.572325104493E+00 WCA energy for atom 8: -1.604626551065E+00 WCA energy for atom 9: -1.586431484963E+00 WCA energy for atom 10: -1.554291291374E+00 WCA energy for atom 11: -1.574315220751E+00 WCA energy for atom 12: -1.604941679892E+00 Total WCA energy: -44.471 kJ/mol Total non-polar energy = 9.363673200142E+00 kJ/mol ---------------------------------------- CALCULATION #5 (solvated-ethane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 5.995981536705E+00 SASA for atom 1: 5.966113633657E+00 SASA for atom 2: 2.121552620704E+01 SASA for atom 3: 2.124158310486E+01 SASA for atom 4: 2.125200586399E+01 SASA for atom 5: 2.123116034573E+01 SASA for atom 6: 2.125200586399E+01 SASA for atom 7: 2.127285138225E+01 Total solvent accessible surface area: 139.427 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 5.096584306199E-02 Surface tension*area energy for atom 1: 5.071196588609E-02 Surface tension*area energy for atom 2: 1.803319727598E-01 Surface tension*area energy for atom 3: 1.805534563913E-01 Surface tension*area energy for atom 4: 1.806420498439E-01 Surface tension*area energy for atom 5: 1.804648629387E-01 Surface tension*area energy for atom 6: 1.806420498439E-01 Surface tension*area energy for atom 7: 1.808192367491E-01 Total surface tension energy: 1.18513 kJ/mol Total solvent accessible volume: 140.346 A^3 Total pressure*volume energy: 33.5988 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -7.360066353115E+00 WCA energy for atom 1: -7.355483516201E+00 WCA energy for atom 2: -1.776106201066E+00 WCA energy for atom 3: -1.773973940651E+00 WCA energy for atom 4: -1.775401936843E+00 WCA energy for atom 5: -1.773464835521E+00 WCA energy for atom 6: -1.774382856097E+00 WCA energy for atom 7: -1.772366599434E+00 Total WCA energy: -25.3612 kJ/mol Total non-polar energy = 9.422717598546E+00 kJ/mol ---------------------------------------- CALCULATION #6 (solvated-hexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 2.986790304710E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.381536722546E+01 SASA for atom 12: 1.384142412329E+01 SASA for atom 13: 7.765654792245E-01 SASA for atom 14: 1.684839013200E+01 SASA for atom 15: 1.682233323417E+01 SASA for atom 16: 4.166572475070E+00 SASA for atom 17: 2.179398933870E+01 SASA for atom 18: 1.877660057086E+01 SASA for atom 19: 1.876096643216E+01 Total solvent accessible surface area: 250.291 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 2.538771759003E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.174306214164E-01 Surface tension*area energy for atom 12: 1.176521050479E-01 Surface tension*area energy for atom 13: 6.600806573408E-03 Surface tension*area energy for atom 14: 1.432113161220E-01 Surface tension*area energy for atom 15: 1.429898324905E-01 Surface tension*area energy for atom 16: 3.541586603809E-02 Surface tension*area energy for atom 17: 1.852489093789E-01 Surface tension*area energy for atom 18: 1.596011048523E-01 Surface tension*area energy for atom 19: 1.594682146734E-01 Total surface tension energy: 2.12748 kJ/mol Total solvent accessible volume: 298.053 A^3 Total pressure*volume energy: 71.3539 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.635406071935E+00 WCA energy for atom 1: -5.957247427848E+00 WCA energy for atom 2: -5.524801144538E+00 WCA energy for atom 3: -5.522294168859E+00 WCA energy for atom 4: -1.605314409440E+00 WCA energy for atom 5: -1.701051761776E+00 WCA energy for atom 6: -1.606669162773E+00 WCA energy for atom 7: -1.442505934938E+00 WCA energy for atom 8: -1.443059002759E+00 WCA energy for atom 9: -1.328947132810E+00 WCA energy for atom 10: -1.328906972440E+00 WCA energy for atom 11: -1.331566344214E+00 WCA energy for atom 12: -1.328041776815E+00 WCA energy for atom 13: -5.937562025661E+00 WCA energy for atom 14: -1.442277774427E+00 WCA energy for atom 15: -1.442777091510E+00 WCA energy for atom 16: -6.602262542378E+00 WCA energy for atom 17: -1.698172146664E+00 WCA energy for atom 18: -1.600970858835E+00 WCA energy for atom 19: -1.600841970217E+00 Total WCA energy: -57.0807 kJ/mol Total non-polar energy = 1.640068943201E+01 kJ/mol ---------------------------------------- CALCULATION #7 (solvated-isobutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.464676753463E+00 SASA for atom 1: 1.984493338158E+01 SASA for atom 2: 1.778643845361E+01 SASA for atom 3: 1.671289426332E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 3.531879535319E+00 SASA for atom 6: 1.673895116114E+01 SASA for atom 7: 1.793756846098E+01 SASA for atom 8: 1.973549441072E+01 SASA for atom 9: 1.710895911022E+01 SASA for atom 10: 4.599657069253E+00 SASA for atom 11: 1.937069784121E+01 SASA for atom 12: 1.654613011726E+01 SASA for atom 13: 1.936548646165E+01 Total solvent accessible surface area: 192.744 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.944975240444E-02 Surface tension*area energy for atom 1: 1.686819337434E-01 Surface tension*area energy for atom 2: 1.511847268556E-01 Surface tension*area energy for atom 3: 1.420596012382E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 3.002097605021E-02 Surface tension*area energy for atom 6: 1.422810848697E-01 Surface tension*area energy for atom 7: 1.524693319183E-01 Surface tension*area energy for atom 8: 1.677517024912E-01 Surface tension*area energy for atom 9: 1.454261524369E-01 Surface tension*area energy for atom 10: 3.909708508865E-02 Surface tension*area energy for atom 11: 1.646509316503E-01 Surface tension*area energy for atom 12: 1.406421059967E-01 Surface tension*area energy for atom 13: 1.646066349240E-01 Total surface tension energy: 1.63832 kJ/mol Total solvent accessible volume: 218.943 A^3 Total pressure*volume energy: 52.415 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.381016335247E+00 WCA energy for atom 1: -1.612317964554E+00 WCA energy for atom 2: -1.588013719598E+00 WCA energy for atom 3: -1.532162371190E+00 WCA energy for atom 4: -5.987950445279E+00 WCA energy for atom 5: -6.393089030861E+00 WCA energy for atom 6: -1.533454887042E+00 WCA energy for atom 7: -1.587650918485E+00 WCA energy for atom 8: -1.614083521570E+00 WCA energy for atom 9: -1.442402031577E+00 WCA energy for atom 10: -6.408813541353E+00 WCA energy for atom 11: -1.605830214390E+00 WCA energy for atom 12: -1.529385873788E+00 WCA energy for atom 13: -1.605662490385E+00 Total WCA energy: -40.8218 kJ/mol Total non-polar energy = 1.323144287435E+01 kJ/mol ---------------------------------------- CALCULATION #8 (solvated-methane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.231304303117E+01 SASA for atom 1: 2.323233009850E+01 SASA for atom 2: 2.345641941977E+01 SASA for atom 3: 2.377431357320E+01 SASA for atom 4: 2.264344420771E+01 Total solvent accessible surface area: 105.42 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 1.046608657649E-01 Surface tension*area energy for atom 1: 1.974748058372E-01 Surface tension*area energy for atom 2: 1.993795650680E-01 Surface tension*area energy for atom 3: 2.020816653722E-01 Surface tension*area energy for atom 4: 1.924692757655E-01 Total surface tension energy: 0.896066 kJ/mol Total solvent accessible volume: 95.985 A^3 Total pressure*volume energy: 22.9788 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -8.133807570805E+00 WCA energy for atom 1: -1.962181541765E+00 WCA energy for atom 2: -1.964078319162E+00 WCA energy for atom 3: -1.963015006647E+00 WCA energy for atom 4: -1.957425549100E+00 Total WCA energy: -15.9805 kJ/mol Total non-polar energy = 7.894367190329E+00 kJ/mol ---------------------------------------- CALCULATION #9 (solvated-neopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 2.441701074100E+00 SASA for atom 1: 1.663993494942E+01 SASA for atom 2: 1.715586152630E+01 SASA for atom 3: 1.645753666466E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 2.389432243768E+00 SASA for atom 6: 1.638457735076E+01 SASA for atom 7: 1.667641460637E+01 SASA for atom 8: 1.721839808108E+01 SASA for atom 9: 2.419300146815E+00 SASA for atom 10: 1.640021148945E+01 SASA for atom 11: 1.666599184724E+01 SASA for atom 12: 1.719234118325E+01 SASA for atom 13: 2.449168049862E+00 SASA for atom 14: 1.723403221977E+01 SASA for atom 15: 1.639500010989E+01 SASA for atom 16: 1.663472356985E+01 Total solvent accessible surface area: 210.755 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.075445912985E-02 Surface tension*area energy for atom 1: 1.414394470700E-01 Surface tension*area energy for atom 2: 1.458248229736E-01 Surface tension*area energy for atom 3: 1.398890616496E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 2.031017407203E-02 Surface tension*area energy for atom 6: 1.392689074814E-01 Surface tension*area energy for atom 7: 1.417495241541E-01 Surface tension*area energy for atom 8: 1.463563836891E-01 Surface tension*area energy for atom 9: 2.056405124793E-02 Surface tension*area energy for atom 10: 1.394017976603E-01 Surface tension*area energy for atom 11: 1.416609307015E-01 Surface tension*area energy for atom 12: 1.461349000577E-01 Surface tension*area energy for atom 13: 2.081792842383E-02 Surface tension*area energy for atom 14: 1.464892738680E-01 Surface tension*area energy for atom 15: 1.393575009340E-01 Surface tension*area energy for atom 16: 1.413951503437E-01 Total surface tension energy: 1.79141 kJ/mol Total solvent accessible volume: 251.127 A^3 Total pressure*volume energy: 60.1198 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.011082520236E+00 WCA energy for atom 1: -1.497367782613E+00 WCA energy for atom 2: -1.498546483218E+00 WCA energy for atom 3: -1.492562171495E+00 WCA energy for atom 4: -5.447325863939E+00 WCA energy for atom 5: -6.004516149175E+00 WCA energy for atom 6: -1.492776531092E+00 WCA energy for atom 7: -1.496078170066E+00 WCA energy for atom 8: -1.501529655270E+00 WCA energy for atom 9: -5.996267554365E+00 WCA energy for atom 10: -1.492194267752E+00 WCA energy for atom 11: -1.496027211216E+00 WCA energy for atom 12: -1.500561393960E+00 WCA energy for atom 13: -6.000218612907E+00 WCA energy for atom 14: -1.500859921426E+00 WCA energy for atom 15: -1.492908499790E+00 WCA energy for atom 16: -1.494057174414E+00 Total WCA energy: -47.4149 kJ/mol Total non-polar energy = 1.449633815052E+01 kJ/mol ---------------------------------------- CALCULATION #10 (solvated-pentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 7.466975761774E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.685881289113E+01 SASA for atom 12: 1.687444702982E+01 SASA for atom 13: 4.196440378117E+00 SASA for atom 14: 1.881308022781E+01 SASA for atom 15: 1.882350298694E+01 SASA for atom 16: 2.182004623652E+01 Total solvent accessible surface area: 222.524 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 6.346929397508E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.432999095746E-01 Surface tension*area energy for atom 12: 1.434327997535E-01 Surface tension*area energy for atom 13: 3.566974321399E-02 Surface tension*area energy for atom 14: 1.599111819364E-01 Surface tension*area energy for atom 15: 1.599997753890E-01 Surface tension*area energy for atom 16: 1.854703930104E-01 Total surface tension energy: 1.89145 kJ/mol Total solvent accessible volume: 258.93 A^3 Total pressure*volume energy: 61.9878 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.655804319869E+00 WCA energy for atom 1: -6.027315962813E+00 WCA energy for atom 2: -5.696430965386E+00 WCA energy for atom 3: -6.016749084714E+00 WCA energy for atom 4: -1.608595384643E+00 WCA energy for atom 5: -1.703300955380E+00 WCA energy for atom 6: -1.609931495887E+00 WCA energy for atom 7: -1.457107525189E+00 WCA energy for atom 8: -1.457741620594E+00 WCA energy for atom 9: -1.354235498709E+00 WCA energy for atom 10: -1.354106470090E+00 WCA energy for atom 11: -1.456736412636E+00 WCA energy for atom 12: -1.455995435596E+00 WCA energy for atom 13: -6.633650611186E+00 WCA energy for atom 14: -1.605996088477E+00 WCA energy for atom 15: -1.606549890103E+00 WCA energy for atom 16: -1.700042300035E+00 Total WCA energy: -49.4003 kJ/mol Total non-polar energy = 1.447900211546E+01 kJ/mol ---------------------------------------- CALCULATION #11 (solvated-propane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.173464698754E+00 SASA for atom 1: 1.931858404557E+01 SASA for atom 2: 2.014198201675E+01 SASA for atom 3: 2.149694070352E+01 SASA for atom 4: 1.904078819252E+00 SASA for atom 5: 2.067354273233E+01 SASA for atom 6: 1.937590922077E+01 SASA for atom 7: 3.098794941136E+00 SASA for atom 8: 1.942802301642E+01 SASA for atom 9: 1.973028303116E+01 SASA for atom 10: 2.204934693736E+01 Total solvent accessible surface area: 170.391 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.697444993941E-02 Surface tension*area energy for atom 1: 1.642079643873E-01 Surface tension*area energy for atom 2: 1.712068471424E-01 Surface tension*area energy for atom 3: 1.827239959799E-01 Surface tension*area energy for atom 4: 1.618466996365E-02 Surface tension*area energy for atom 5: 1.757251132248E-01 Surface tension*area energy for atom 6: 1.646952283766E-01 Surface tension*area energy for atom 7: 2.633975699966E-02 Surface tension*area energy for atom 8: 1.651381956396E-01 Surface tension*area energy for atom 9: 1.677074057649E-01 Surface tension*area energy for atom 10: 1.874194489675E-01 Total surface tension energy: 1.44832 kJ/mol Total solvent accessible volume: 183.573 A^3 Total pressure*volume energy: 43.9474 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.818670105515E+00 WCA energy for atom 1: -1.641297645338E+00 WCA energy for atom 2: -1.649584120441E+00 WCA energy for atom 3: -1.711408141255E+00 WCA energy for atom 4: -6.624720142882E+00 WCA energy for atom 5: -1.610117050515E+00 WCA energy for atom 6: -1.596858009746E+00 WCA energy for atom 7: -6.816460624835E+00 WCA energy for atom 8: -1.642782751806E+00 WCA energy for atom 9: -1.645779566650E+00 WCA energy for atom 10: -1.714436154542E+00 Total WCA energy: -33.4721 kJ/mol Total non-polar energy = 1.192358496286E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print APOL energy 1 (solvated-2-methylbutane) end Global net APOL energy = 1.439739455792E+01 kJ/mol print APOL energy 2 (solvated-butane) end Global net APOL energy = 1.208346456826E+01 kJ/mol print APOL energy 3 (solvated-cyclohexane) end Global net APOL energy = 1.354016672221E+01 kJ/mol print APOL energy 4 (solvated-cyclopentane) end Global net APOL energy = 9.363673200142E+00 kJ/mol print APOL energy 5 (solvated-ethane) end Global net APOL energy = 9.422717598546E+00 kJ/mol print APOL energy 6 (solvated-hexane) end Global net APOL energy = 1.640068943201E+01 kJ/mol print APOL energy 7 (solvated-isobutane) end Global net APOL energy = 1.323144287435E+01 kJ/mol print APOL energy 8 (solvated-methane) end Global net APOL energy = 7.894367190329E+00 kJ/mol print APOL energy 9 (solvated-neopentane) end Global net APOL energy = 1.449633815052E+01 kJ/mol print APOL energy 10 (solvated-pentane) end Global net APOL energy = 1.447900211546E+01 kJ/mol print APOL energy 11 (solvated-propane) end Global net APOL energy = 1.192358496286E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 11 molecules Final memory usage: 0.001 MB total, 2.267 MB high water Thanks for using APBS! Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) *** PASSED *** Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) *** PASSED *** Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) *** PASSED *** Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) *** PASSED *** Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) *** PASSED *** Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) *** PASSED *** Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) *** PASSED *** Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) *** PASSED *** Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) *** PASSED *** Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) *** PASSED *** Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) *** PASSED *** Elapsed time: 11.462178 seconds -------------------------------------------------------------------------------- Total elapsed time: 11.462178 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-mol.in Checking for intermediate energies in input file alkanes.out EXPECTED COMPUTED: 11 EXPECTED EXPECTED: 11 COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] EXPECTED: ['1.439739455792E+01', '1.208346456826E+01', '1.354016672221E+01', '9.363673200142E+00', '9.422717598546E+00', '1.640068943201E+01', '1.323144287435E+01', '7.894367190329E+00', '1.449633815052E+01', '1.447900211546E+01', '1.192358496286E+01'] COMPUTED RESULT 14.39739455792 COMPUTED RESULT 12.08346456826 COMPUTED RESULT 13.54016672221 COMPUTED RESULT 9.363673200142 COMPUTED RESULT 9.422717598546 COMPUTED RESULT 16.40068943201 COMPUTED RESULT 13.23144287435 COMPUTED RESULT 7.894367190329 COMPUTED RESULT 14.49633815052 COMPUTED RESULT 14.47900211546 COMPUTED RESULT 11.92358496286 Running tests for FKBP section BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-mol.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7h-dmso-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file 1d7h-dmso-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.060899690259E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.276523673491E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.961107503213E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.121048606059E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.058410584089E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.205385249581E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.335429017008E+03 kJ/mol Global net ELEC energy = -3.335429017008E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.180527370616E+01 kJ/mol Global net ELEC energy = -2.180527370616E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.328631844166E+03 kJ/mol Global net ELEC energy = -3.328631844166E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.500810086371E+01 kJ/mol Global net ELEC energy = 1.500810086371E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04) *** PASSED *** Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) *** PASSED *** Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) *** PASSED *** Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) *** PASSED *** Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) *** PASSED *** Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) *** PASSED *** Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) *** PASSED *** Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) *** PASSED *** Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) *** PASSED *** Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) *** PASSED *** Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) *** PASSED *** Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) *** PASSED *** Testing computed result against expected result (1.500810086371e+01, 1.500810086371e+01) *** PASSED *** Elapsed time: 12.03944 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-smol.in Checking for intermediate energies in input file 1d7h-dmso-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [10608.99690259, 42765.23673491, 13992.34956777, 46100.66575192, 39.61107503213, 712.1048606059, 67.51571424823, 733.9101343121, 10584.10584089, 42053.85249581, 13959.61902233, 45382.48433997, -3335.429017008, -21.80527370616, -3328.631844166, 15.00810086371] EXPECTED: ['1.060899690259E+04', '4.276523673491E+04', '1.399234956777E+04', '4.610066575192E+04', '3.961107503213E+01', '7.121048606059E+02', '6.751571424823E+01', '7.339101343121E+02', '1.058410584089E+04', '4.205385249581E+04', '1.395961902233E+04', '4.538248433997E+04', '*', '*', '*', '1.500810086371E+01'] COMPUTED RESULT 10608.99690259 COMPUTED RESULT 42765.23673491 COMPUTED RESULT 13992.34956777 COMPUTED RESULT 46100.66575192 COMPUTED RESULT 39.61107503213 COMPUTED RESULT 712.1048606059 COMPUTED RESULT 67.51571424823 COMPUTED RESULT 733.9101343121 COMPUTED RESULT 10584.10584089 COMPUTED RESULT 42053.85249581 COMPUTED RESULT 13959.61902233 COMPUTED RESULT 45382.48433997 COMPUTED RESULT -3335.429017008 COMPUTED RESULT -21.80527370616 COMPUTED RESULT -3328.631844166 COMPUTED RESULT 15.00810086371 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-smol.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7h-dmso-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file 1d7h-dmso-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.074948704824E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.289487256481E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.719709905887E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.125747080979E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.071654753674E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.218178203716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.205793187109E+03 kJ/mol Global net ELEC energy = -3.205793187109E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.133542621421E+01 kJ/mol Global net ELEC energy = -2.133542621421E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.200702302816E+03 kJ/mol Global net ELEC energy = -3.200702302816E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.624454192073E+01 kJ/mol Global net ELEC energy = 1.624454192073E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) *** PASSED *** Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) *** PASSED *** Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) *** PASSED *** Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) *** PASSED *** Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) *** PASSED *** Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) *** PASSED *** Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) *** PASSED *** Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) *** PASSED *** Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) *** PASSED *** Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) *** PASSED *** Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) *** PASSED *** Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) *** PASSED *** Testing computed result against expected result (1.624454192073e+01, 1.624454192072e+01) *** PASSED *** Elapsed time: 11.803305 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-mol.in Checking for intermediate energies in input file 1d7h-dmso-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [10749.48704824, 42894.87256481, 13992.34956777, 46100.66575192, 37.19709905887, 712.5747080979, 67.51571424823, 733.9101343121, 10716.54753674, 42181.78203716, 13959.61902233, 45382.48433997, -3205.793187109, -21.33542621421, -3200.702302816, 16.24454192073] EXPECTED: ['1.074948704824E+04', '4.289487256481E+04', '1.399234956777E+04', '4.610066575192E+04', '3.719709905887E+01', '7.125747080979E+02', '6.751571424823E+01', '7.339101343121E+02', '1.071654753674E+04', '4.218178203716E+04', '1.395961902233E+04', '4.538248433997E+04', '*', '*', '*', '1.624454192072E+01'] COMPUTED RESULT 10749.48704824 COMPUTED RESULT 42894.87256481 COMPUTED RESULT 13992.34956777 COMPUTED RESULT 46100.66575192 COMPUTED RESULT 37.19709905887 COMPUTED RESULT 712.5747080979 COMPUTED RESULT 67.51571424823 COMPUTED RESULT 733.9101343121 COMPUTED RESULT 10716.54753674 COMPUTED RESULT 42181.78203716 COMPUTED RESULT 13959.61902233 COMPUTED RESULT 45382.48433997 COMPUTED RESULT -3205.793187109 COMPUTED RESULT -21.33542621421 COMPUTED RESULT -3200.702302816 COMPUTED RESULT 16.24454192073 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-mol.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7i-dss-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file 1d7i-dss-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.160578033846E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.955701871716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.431133325426E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677348113184E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.040108332204E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.787747796627E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.460997931137E+03 kJ/mol Global net ELEC energy = -3.460997931137E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.052167100108E+01 kJ/mol Global net ELEC energy = -2.052167100108E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -3.454901259473E+03 kJ/mol Global net ELEC energy = -3.454901259473E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.442499933668E+01 kJ/mol Global net ELEC energy = 1.442499933668E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) *** PASSED *** Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) *** PASSED *** Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) *** PASSED *** Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) *** PASSED *** Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) *** PASSED *** Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) *** PASSED *** Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) *** PASSED *** Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) *** PASSED *** Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) *** PASSED *** Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) *** PASSED *** Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) *** PASSED *** Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) *** PASSED *** Testing computed result against expected result (1.442499933668e+01, 1.442500529301e+01) *** PASSED *** Elapsed time: 19.375898 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-smol.in Checking for intermediate energies in input file 1d7i-dss-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [9160.578033846, 39557.01871716, 12649.65939588, 43018.01664829, 94.31133325426, 1677.348113184, 117.1079106781, 1697.869784185, 9040.108332204, 37877.47796627, 12524.95566243, 41332.37922574, -3460.997931137, -20.52167100108, -3454.901259473, 14.42499933668] EXPECTED: ['9.160578033846E+03', '3.955701871716E+04', '1.264965939588E+04', '4.301801664829E+04', '9.431133325426E+01', '1.677348113184E+03', '1.171079106781E+02', '1.697869784185E+03', '9.040108332204E+03', '3.787747796627E+04', '1.252495566243E+04', '4.133237922574E+04', '*', '*', '*', '1.442500529301E+01'] COMPUTED RESULT 9160.578033846 COMPUTED RESULT 39557.01871716 COMPUTED RESULT 12649.65939588 COMPUTED RESULT 43018.01664829 COMPUTED RESULT 94.31133325426 COMPUTED RESULT 1677.348113184 COMPUTED RESULT 117.1079106781 COMPUTED RESULT 1697.869784185 COMPUTED RESULT 9040.108332204 COMPUTED RESULT 37877.47796627 COMPUTED RESULT 12524.95566243 COMPUTED RESULT 41332.37922574 COMPUTED RESULT -3460.997931137 COMPUTED RESULT -20.52167100108 COMPUTED RESULT -3454.901259473 COMPUTED RESULT 14.42499933668 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-smol.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7i-dss-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file 1d7i-dss-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.634884642408E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.003177540425E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.942232645345E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677798535473E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.507068451372E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.835075772299E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -2.986241244040E+03 kJ/mol Global net ELEC energy = -2.986241244040E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.007124871262E+01 kJ/mol Global net ELEC energy = -2.007124871262E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -2.981621502756E+03 kJ/mol Global net ELEC energy = -2.981621502756E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.545150742844E+01 kJ/mol Global net ELEC energy = 1.545150742844E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) *** PASSED *** Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) *** PASSED *** Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) *** PASSED *** Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) *** PASSED *** Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) *** PASSED *** Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) *** PASSED *** Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) *** PASSED *** Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) *** PASSED *** Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) *** PASSED *** Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) *** PASSED *** Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) *** PASSED *** Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) *** PASSED *** Testing computed result against expected result (1.545150742844e+01, 1.545150009785e+01) *** PASSED *** Elapsed time: 23.579143 seconds -------------------------------------------------------------------------------- Total elapsed time: 66.797786 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file 1d7i-dss-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [9634.884642408, 40031.77540425, 12649.65939588, 43018.01664829, 79.42232645345, 1677.798535473, 117.1079106781, 1697.869784185, 9507.068451372, 38350.75772299, 12524.95566243, 41332.37922574, -2986.24124404, -20.07124871262, -2981.621502756, 15.45150742844] EXPECTED: ['9.634884642408E+03', '4.003177540425E+04', '1.264965939588E+04', '4.301801664829E+04', '7.942232645345E+01', '1.677798535473E+03', '1.171079106781E+02', '1.697869784185E+03', '9.507068451372E+03', '3.835075772299E+04', '1.252495566243E+04', '4.133237922574E+04', '*', '*', '*', '1.545150009785E+01'] COMPUTED RESULT 9634.884642408 COMPUTED RESULT 40031.77540425 COMPUTED RESULT 12649.65939588 COMPUTED RESULT 43018.01664829 COMPUTED RESULT 79.42232645345 COMPUTED RESULT 1677.798535473 COMPUTED RESULT 117.1079106781 COMPUTED RESULT 1697.869784185 COMPUTED RESULT 9507.068451372 COMPUTED RESULT 38350.75772299 COMPUTED RESULT 12524.95566243 COMPUTED RESULT 41332.37922574 COMPUTED RESULT -2986.24124404 COMPUTED RESULT -20.07124871262 COMPUTED RESULT -2981.621502756 COMPUTED RESULT 15.45150742844 Running tests for hca-bind section BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.213600726771E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.825764811255E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.458471211905E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.093606095527E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.515433544464E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.786369323561E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.105322784838E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.533304996252E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850429388099E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.246475812665E+01 kJ/mol Global net ELEC energy = -5.246475812665E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02) *** PASSED *** Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) *** PASSED *** Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) *** PASSED *** Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) *** PASSED *** Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) *** PASSED *** Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) *** PASSED *** Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) *** PASSED *** Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) *** PASSED *** Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) *** PASSED *** Testing computed result against expected result (-5.246475812665e+01, -5.246475812665e+01) *** PASSED *** Elapsed time: 17.255348 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 10 EXPECTED EXPECTED: 10 COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812665] EXPECTED: ['2.213600726771E+02', '1.825764811255E+03', '6.458471211905E+03', '2.093606095527E+04', '1.515433544464E+05', '1.786369323561E+05', '2.105322784838E+04', '1.533304996252E+05', '1.850429388099E+05', '-5.246475812665E+01'] COMPUTED RESULT 221.3600726771 COMPUTED RESULT 1825.764811255 COMPUTED RESULT 6458.471211905 COMPUTED RESULT 20936.06095527 COMPUTED RESULT 151543.3544464 COMPUTED RESULT 178636.9323561 COMPUTED RESULT 21053.22784838 COMPUTED RESULT 153330.4996252 COMPUTED RESULT 185042.9388099 COMPUTED RESULT -52.46475812665 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.884888131017E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.820045922544E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.460002606908E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189161497021E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.520000494925E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.790436191580E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.195842512312E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.537771604355E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.854495619747E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.405979017066E+01 kJ/mol Global net ELEC energy = -5.405979017066E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02) *** PASSED *** Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) *** PASSED *** Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) *** PASSED *** Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) *** PASSED *** Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) *** PASSED *** Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) *** PASSED *** Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) *** PASSED *** Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) *** PASSED *** Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) *** PASSED *** Testing computed result against expected result (-5.405979017066e+01, -5.405977880082e+01) *** PASSED *** Elapsed time: 13.648825 seconds -------------------------------------------------------------------------------- Total elapsed time: 30.904173 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 10 EXPECTED EXPECTED: 10 COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017066] EXPECTED: ['1.884888131017E+02', '1.820045922544E+03', '6.460002606908E+03', '2.189161497021E+04', '1.520000494925E+05', '1.790436191580E+05', '2.195842512312E+04', '1.537771604355E+05', '1.854495619747E+05', '-5.405977880082E+01'] COMPUTED RESULT 188.4888131017 COMPUTED RESULT 1820.045922544 COMPUTED RESULT 6460.002606908 COMPUTED RESULT 21891.61497021 COMPUTED RESULT 152000.0494925 COMPUTED RESULT 179043.619158 COMPUTED RESULT 21958.42512312 COMPUTED RESULT 153777.1604355 COMPUTED RESULT 185449.5619747 COMPUTED RESULT -54.05979017066 Running tests for ionize section BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acetic-acid.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading PQR-format atom data from acetate.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading PQR-format atom data from proton.pqr. 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.823898055191E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793274462353E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.219846763777E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392741988698E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.862359524598E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.288156251610E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.267882018629E+01 kJ/mol Global net ELEC energy = -2.267882018629E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.997462636633E+02 kJ/mol Global net ELEC energy = -1.997462636633E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.974598403628E+02 kJ/mol Global net ELEC energy = -2.974598403628E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.745272838398E+02 kJ/mol Global net ELEC energy = -4.745272838398E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Testing computed result against expected result (5.823898055191e+03, 5.823898055191e+03) *** PASSED *** Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) *** PASSED *** Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) *** PASSED *** Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) *** PASSED *** Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) *** PASSED *** Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) *** PASSED *** Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) *** PASSED *** Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) *** PASSED *** Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) *** PASSED *** Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) *** PASSED *** Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) *** PASSED *** Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) *** PASSED *** Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) *** PASSED *** Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) *** PASSED *** Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) *** PASSED *** Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) *** PASSED *** Elapsed time: 10.320291 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [5823.898055191, 9793.274462353, 5846.917564309, 9815.953282539, 8219.846763777, 13927.41988698, 8420.373979905, 14127.16615065, 3862.359524598, 6288.15625161, 4162.533113906, 6585.616091973, -22.67882018629, -199.7462636633, -297.4598403628, -474.5272838398] EXPECTED: ['5.823898055191E+03', '9.793274462353E+03', '5.846917564309E+03', '9.815953282539E+03', '8.219846763777E+03', '1.392741988698E+04', '8.420373979905E+03', '1.412716615065E+04', '3.862359524598E+03', '6.288156251610E+03', '4.162533113906E+03', '6.585616091973E+03', '-2.267881997628E+01', '-1.997462580204E+02', '-2.974598331751E+02', '-4.745272868358E+02'] COMPUTED RESULT 5823.898055191 COMPUTED RESULT 9793.274462353 COMPUTED RESULT 5846.917564309 COMPUTED RESULT 9815.953282539 COMPUTED RESULT 8219.846763777 COMPUTED RESULT 13927.41988698 COMPUTED RESULT 8420.373979905 COMPUTED RESULT 14127.16615065 COMPUTED RESULT 3862.359524598 COMPUTED RESULT 6288.15625161 COMPUTED RESULT 4162.533113906 COMPUTED RESULT 6585.616091973 COMPUTED RESULT -22.67882018629 COMPUTED RESULT -199.7462636633 COMPUTED RESULT -297.4598403628 COMPUTED RESULT -474.5272838398 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acetic-acid.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading PQR-format atom data from acetate.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading PQR-format atom data from proton.pqr. 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.824172730822E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793622759239E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.221328580569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392867783119E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.863066835285E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.289649216644E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.233052329981E+01 kJ/mol Global net ELEC energy = -2.233052329981E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.984883194538E+02 kJ/mol Global net ELEC energy = -1.984883194538E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.959668753288E+02 kJ/mol Global net ELEC energy = -2.959668753288E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.721246714828E+02 kJ/mol Global net ELEC energy = -4.721246714828E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Testing computed result against expected result (5.824172730822e+03, 5.824172730822e+03) *** PASSED *** Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) *** PASSED *** Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) *** PASSED *** Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) *** PASSED *** Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) *** PASSED *** Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) *** PASSED *** Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) *** PASSED *** Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) *** PASSED *** Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) *** PASSED *** Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) *** PASSED *** Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) *** PASSED *** Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) *** PASSED *** Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) *** PASSED *** Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) *** PASSED *** Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) *** PASSED *** Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) *** PASSED *** Elapsed time: 10.578655 seconds -------------------------------------------------------------------------------- Total elapsed time: 20.898946 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file ion-pmf.in Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [5824.172730822, 9793.622759239, 5846.917564309, 9815.953282539, 8221.328580569, 13928.67783119, 8420.373979905, 14127.16615065, 3863.066835285, 6289.649216644, 4162.533113906, 6585.616091973, -22.33052329981, -198.4883194538, -295.9668753288, -472.1246714828] EXPECTED: ['5.824172730822E+03', '9.793622759239E+03', '5.846917564309E+03', '9.815953282539E+03', '8.221328580569E+03', '1.392867783119E+04', '8.420373979905E+03', '1.412716615065E+04', '3.863066835285E+03', '6.289649216644E+03', '4.162533113906E+03', '6.585616091973E+03', '-2.233050451129E+01', '-1.984883191396E+02', '-2.959668653531E+02', '-4.721247084138E+02'] COMPUTED RESULT 5824.172730822 COMPUTED RESULT 9793.622759239 COMPUTED RESULT 5846.917564309 COMPUTED RESULT 9815.953282539 COMPUTED RESULT 8221.328580569 COMPUTED RESULT 13928.67783119 COMPUTED RESULT 8420.373979905 COMPUTED RESULT 14127.16615065 COMPUTED RESULT 3863.066835285 COMPUTED RESULT 6289.649216644 COMPUTED RESULT 4162.533113906 COMPUTED RESULT 6585.616091973 COMPUTED RESULT -22.33052329981 COMPUTED RESULT -198.4883194538 COMPUTED RESULT -295.9668753288 COMPUTED RESULT -472.1246714828 Running tests for ion-pmf section BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: ion-pmf.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'ion-pmf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file ion-pmf.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 1 molecules Reading PDB-format atom data from ion-pmf.pdb. Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.106 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 7.839535983197E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! ---------------------------------------- CALCULATION #2 (ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.155 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 8.964727588811E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 0.000e+00 0.000e+00 0.000e+00 mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 0.000e+00 0.000e+00 0.000e+00 ---------------------------------------- CALCULATION #3 (asolv): APOLAR Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n gamma 0.000720 pressure 0.000000 bconc 0.033000 tot 0 2.715e-02 9.130e-07 9.130e-07 sasa 0 -1.100e+01 0.000e+00 0.000e+00 sav 0 0.000e+00 0.000e+00 0.000e+00 wca 0 -5.827e-01 -2.767e-05 -2.767e-05 tot 1 -2.723e-02 9.133e-07 9.133e-07 sasa 1 1.112e+01 0.000e+00 0.000e+00 sav 1 0.000e+00 0.000e+00 0.000e+00 wca 1 5.827e-01 -2.767e-05 -2.767e-05 Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.153275282828E+02 SASA for atom 1: 1.153114143344E+02 Total solvent accessible surface area: 230.639 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.303582036361E-02 Surface tension*area energy for atom 1: 8.302421832080E-02 Total surface tension energy: 0.16606 kJ/mol Total solvent accessible volume: 0 A^3 Total pressure*volume energy: 0 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.909718359932E+00 WCA energy for atom 1: -6.909422551724E+00 Total WCA energy: -13.8191 kJ/mol Total non-polar energy = -1.365308087297E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print energy 1 (solv) - 2 (ref) end Local net energy (PE 0) = -1.125191605614E+03 kJ/mol Global net ELEC energy = -1.125191605614E+03 kJ/mol print force 1 (solv) - 2 (ref) end Printing per-atom forces (kJ/mol/A). Legend: tot n -- Total force for atom n qf n -- Fixed charge force for atom n db n -- Dielectric boundary force for atom n ib n -- Ionic boundary force for atom n tot all -- Total force for system qf 0 8.398642197666E+01 -1.324564548552E-05 -1.613435632529E-05 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 0 6.148357059184E+00 -2.667517425897E-05 -5.378919678211E-05 tot 0 9.013477903584E+01 -3.992081974449E-05 -6.992355310740E-05 qf 1 -8.466423642736E+01 -1.836748045969E-05 -3.062224428458E-05 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 1 2.882739230548E+00 -3.149946357588E-05 -6.291495506459E-05 tot 1 -8.178149719681E+01 -4.986694403557E-05 -9.353719934917E-05 tot all 8.353281839029E+00 -8.978776378007E-05 -1.634607524566E-04 print APOL energy 1 (asolv) end Global net APOL energy = -1.365308087297E+01 kJ/mol print APOL force 1 (asolv) end Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n tot all -- Total force for system sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 0 -5.826577086437E-01 -2.766670515801E-05 -2.766670515838E-05 tot 0 -1.158042745197E+01 -2.766670515801E-05 -2.766670515838E-05 sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 1 5.826560767576E-01 -2.767485007141E-05 -2.767485007183E-05 tot 1 1.170128043265E+01 -2.767485007141E-05 -2.767485007183E-05 tot all 1.208529806779E-01 -5.534155522943E-05 -5.534155523021E-05 ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 60.711 MB total, 62.250 MB high water Thanks for using APBS! Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) *** PASSED *** Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) *** PASSED *** Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) *** PASSED *** Elapsed time: 11.849472 seconds -------------------------------------------------------------------------------- Total elapsed time: 11.849472 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-vdw.in Checking for intermediate energies in input file ion-pmf.out EXPECTED COMPUTED: 4 EXPECTED EXPECTED: 4 COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65308087297] EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] COMPUTED RESULT 7839.535983197 COMPUTED RESULT 8964.727588811 COMPUTED RESULT -1125.191605614 COMPUTED RESULT -13.65308087297 Running tests for pka-lig section BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-vdw.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-vdw.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-mol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.224988750664E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.049695084686E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.818450789522E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.008254338259E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.840918409896E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.113304681884E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 8.083515648730E+00 kJ/mol Global net ELEC energy = 8.083515648730E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03) *** PASSED *** Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) *** PASSED *** Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) *** PASSED *** Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) *** PASSED *** Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) *** PASSED *** Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) *** PASSED *** Testing computed result against expected result (8.083515648730e+00, 8.083515648730e+00) *** PASSED *** Elapsed time: 23.9815 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-vdw.in Checking for intermediate energies in input file apbs-mol-vdw.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.08351564873] EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] COMPUTED RESULT 2224.988750664 COMPUTED RESULT 10496.95084686 COMPUTED RESULT 181845.0789522 COMPUTED RESULT 300825.4338259 COMPUTED RESULT 184091.8409896 COMPUTED RESULT 311330.4681884 COMPUTED RESULT 8.08351564873 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-vdw.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-vdw.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-smol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.226793167046E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.050504485887E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827976621645E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.017228546773E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850819075387E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.122488625388E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 2.096300255723E+01 kJ/mol Global net ELEC energy = 2.096300255723E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03) *** PASSED *** Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04) *** PASSED *** Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05) *** PASSED *** Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05) *** PASSED *** Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05) *** PASSED *** Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05) *** PASSED *** Testing computed result against expected result (2.096300255723e+01, 2.096296139195e+01) *** PASSED *** Elapsed time: 17.788101 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-surf.in Checking for intermediate energies in input file apbs-smol-vdw.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.96300255723] EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] COMPUTED RESULT 2226.793167046 COMPUTED RESULT 10505.04485887 COMPUTED RESULT 182797.6621645 COMPUTED RESULT 301722.8546773 COMPUTED RESULT 185081.9075387 COMPUTED RESULT 312248.8625388 COMPUTED RESULT 20.96300255723 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-surf.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-surf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-mol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.244350164274E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052149475373E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.862615690066E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.051810884053E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.886625455219E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.158218439277E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.192607686581E+02 kJ/mol Global net ELEC energy = 1.192607686581E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) *** PASSED *** Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) *** PASSED *** Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) *** PASSED *** Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) *** PASSED *** Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) *** PASSED *** Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) *** PASSED *** Testing computed result against expected result (1.192607686581e+02, 1.192608095265e+02) *** PASSED *** Elapsed time: 16.680624 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-surf.in Checking for intermediate energies in input file apbs-mol-surf.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686581] EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] COMPUTED RESULT 2244.350164274 COMPUTED RESULT 10521.49475373 COMPUTED RESULT 186261.5690066 COMPUTED RESULT 305181.0884053 COMPUTED RESULT 188662.5455219 COMPUTED RESULT 315821.8439277 COMPUTED RESULT 119.2607686581 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-surf.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-surf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-smol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.251466789420E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052814502873E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.864071689626E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.053319953673E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.888027142979E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.159690177241E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.088773280806E+02 kJ/mol Global net ELEC energy = 1.088773280806E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03) *** PASSED *** Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) *** PASSED *** Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) *** PASSED *** Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) *** PASSED *** Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) *** PASSED *** Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) *** PASSED *** Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) *** PASSED *** Elapsed time: 17.102531 seconds -------------------------------------------------------------------------------- Total elapsed time: 75.552756 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_1.in Checking for intermediate energies in input file apbs-smol-surf.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] COMPUTED RESULT 2251.46678942 COMPUTED RESULT 10528.14502873 COMPUTED RESULT 186407.1689626 COMPUTED RESULT 305331.9953673 COMPUTED RESULT 188802.7142979 COMPUTED RESULT 315969.0177241 COMPUTED RESULT 108.8773280806 Running tests for point-pmf section BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_1.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file complex-0_1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_1.pqr. 2 atoms Centered at (-2.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.975920687031E+01 kJ/mol Fixed charge energy = 89.7592 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 88.6151 kJ/mol Per-atom energies: Atom 0: 8.975920687031E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.058277719334E+02 kJ/mol Fixed charge energy = 205.828 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 201.106 kJ/mol Per-atom energies: Atom 0: 1.069144350786E+02 kJ/mol Atom 1: 9.891333685475E+01 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 1.830820799027E+01 kJ/mol Global net ELEC energy = 1.830820799027E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.067 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) *** PASSED *** Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) *** PASSED *** Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) *** PASSED *** Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) *** PASSED *** Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) *** PASSED *** Elapsed time: 2.118724 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_2.in Checking for intermediate energies in input file complex-0_1.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 89.75920687031, 205.8277719334, 0.0, 0.0, 0.0, 97.7604, 89.7592, 205.828, 96.5336, 88.6151, 201.106, 18.30820799027] EXPECTED: ['9.776035707281E+01', '8.975920687031E+01', '2.058277719334E+02', '*', '*', '*', '97.7604', '89.7592', '205.828', '96.5336', '88.6151', '201.106', '1.830820799027E+01'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 89.75920687031 COMPUTED RESULT 205.8277719334 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 89.7592 COMPUTED RESULT 205.828 COMPUTED RESULT 96.5336 COMPUTED RESULT 88.6151 COMPUTED RESULT 201.106 COMPUTED RESULT 18.30820799027 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_2.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file complex-0_2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_2.pqr. 2 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.656 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.084282010393E+02 kJ/mol Fixed charge energy = 208.428 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 203.83 kJ/mol Per-atom energies: Atom 0: 1.022136878480E+02 kJ/mol Atom 1: 1.062145131913E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 8.906694086750E+00 kJ/mol Global net ELEC energy = 8.906694086750E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) *** PASSED *** Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) *** PASSED *** Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) *** PASSED *** Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) *** PASSED *** Testing computed result against expected result (8.906694086750e+00, 8.906694086750e+00) *** PASSED *** Elapsed time: 2.13469 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_3.in Checking for intermediate energies in input file complex-0_2.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 101.7611498797, 208.4282010393, 0.0, 0.0, 0.0, 97.7604, 101.761, 208.428, 96.5336, 100.656, 203.83, 8.90669408675] EXPECTED: ['9.776035707281E+01', '1.017611498797E+02', '2.084282010393E+02', '*', '*', '*', '97.7604', '101.761', '208.428', '96.5336', '100.656', '203.83', '8.906694086750E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 101.7611498797 COMPUTED RESULT 208.4282010393 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 101.761 COMPUTED RESULT 208.428 COMPUTED RESULT 96.5336 COMPUTED RESULT 100.656 COMPUTED RESULT 203.83 COMPUTED RESULT 8.90669408675 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_3.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file complex-0_3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol3.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_3.pqr. 2 atoms Centered at (-1.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.337661883222E+02 kJ/mol Fixed charge energy = 133.766 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 132.672 kJ/mol Per-atom energies: Atom 0: 1.337661883222E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.374361452120E+02 kJ/mol Fixed charge energy = 237.436 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 232.924 kJ/mol Per-atom energies: Atom 0: 1.007151570480E+02 kJ/mol Atom 1: 1.367209881640E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 5.909599816984E+00 kJ/mol Global net ELEC energy = 5.909599816984E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) *** PASSED *** Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) *** PASSED *** Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) *** PASSED *** Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) *** PASSED *** Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) *** PASSED *** Elapsed time: 1.108388 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_4.in Checking for intermediate energies in input file complex-0_3.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 133.7661883222, 237.436145212, 0.0, 0.0, 0.0, 97.7604, 133.766, 237.436, 96.5336, 132.672, 232.924, 5.909599816984] EXPECTED: ['9.776035707281E+01', '1.337661883222E+02', '2.374361452120E+02', '*', '*', '*', '97.7604', '133.766', '237.436', '96.5336', '132.672', '232.924', '5.909599816984E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 133.7661883222 COMPUTED RESULT 237.436145212 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 133.766 COMPUTED RESULT 237.436 COMPUTED RESULT 96.5336 COMPUTED RESULT 132.672 COMPUTED RESULT 232.924 COMPUTED RESULT 5.909599816984 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_4.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_4.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file complex-0_4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol4.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_4.pqr. 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.654 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.061 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.039516519000E+02 kJ/mol Fixed charge energy = 203.952 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 199.493 kJ/mol Per-atom energies: Atom 0: 9.997541697022E+01 kJ/mol Atom 1: 1.039762349297E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 4.430144947418E+00 kJ/mol Global net ELEC energy = 4.430144947418E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) *** PASSED *** Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) *** PASSED *** Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) *** PASSED *** Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) *** PASSED *** Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) *** PASSED *** Elapsed time: 1.359769 seconds -------------------------------------------------------------------------------- Total elapsed time: 6.721571 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file complex-0_4.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 101.7611498797, 203.9516519, 0.0, 0.0, 0.0, 97.7604, 101.761, 203.952, 96.5336, 100.654, 199.493, 4.430144947418] EXPECTED: ['9.776035707281E+01', '1.017611498797E+02', '2.039516519000E+02', '*', '*', '*', '97.7604', '101.761', '203.952', '96.5336', '100.654', '199.493', '4.430144947418E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 101.7611498797 COMPUTED RESULT 203.9516519 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 101.761 COMPUTED RESULT 203.952 COMPUTED RESULT 96.5336 COMPUTED RESULT 100.654 COMPUTED RESULT 199.493 COMPUTED RESULT 4.430144947418 Running tests for solv section BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847663548071E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.883912182952E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.732623683321E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.123035854133E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.624863488074E+01 kJ/mol Global net ELEC energy = -3.624863488074E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.904121708125E+02 kJ/mol Global net ELEC energy = -3.904121708125E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.541635359318E+02 kJ/mol Global net ELEC energy = -3.541635359318E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03) *** PASSED *** Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) *** PASSED *** Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) *** PASSED *** Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) *** PASSED *** Testing computed result against expected result (-3.624863488074e+01, -3.624863445503e+01) *** PASSED *** Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) *** PASSED *** Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) *** PASSED *** Elapsed time: 2.587109 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488074, -390.4121708125, -354.1635359318] EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] COMPUTED RESULT 1847.663548071 COMPUTED RESULT 1883.912182952 COMPUTED RESULT 2732.623683321 COMPUTED RESULT 3123.035854133 COMPUTED RESULT -36.24863488074 COMPUTED RESULT -390.4121708125 COMPUTED RESULT -354.1635359318 BINARY: /build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/apbs-A5U5s9/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on May 31 2022 at 00:52:47 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847860440020E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.885436377745E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.734040568569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.125279428954E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.757593772493E+01 kJ/mol Global net ELEC energy = -3.757593772493E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.912388603848E+02 kJ/mol Global net ELEC energy = -3.912388603848E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.536629226599E+02 kJ/mol Global net ELEC energy = -3.536629226599E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03) *** PASSED *** Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) *** PASSED *** Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) *** PASSED *** Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) *** PASSED *** Testing computed result against expected result (-3.757593772493e+01, -3.757593797629e+01) *** PASSED *** Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) *** PASSED *** Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) *** PASSED *** Elapsed time: 1.663685 seconds -------------------------------------------------------------------------------- Total elapsed time: 4.250794 seconds Test results have been logged -------------------------------------------------------------------------------- Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772493, -391.2388603848, -353.6629226599] EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] COMPUTED RESULT 1847.86044002 COMPUTED RESULT 1885.436377745 COMPUTED RESULT 2734.040568569 COMPUTED RESULT 3125.279428954 COMPUTED RESULT -37.57593772493 COMPUTED RESULT -391.2388603848 COMPUTED RESULT -353.6629226599 make[1]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1' dh_install -i -O--buildsystem=cmake dh_installdocs -i -O--buildsystem=cmake dh_sphinxdoc -i -O--buildsystem=cmake dh_installchangelogs -i -O--buildsystem=cmake dh_installman -i -O--buildsystem=cmake dh_python3 -i -O--buildsystem=cmake E: dh_python3 dh_python3:176: no package to act on (python3-foo or one with ${python3:Depends} in Depends) dh_installsystemduser -i -O--buildsystem=cmake dh_perl -i -O--buildsystem=cmake dh_link -i -O--buildsystem=cmake dh_strip_nondeterminism -i -O--buildsystem=cmake dh_compress -i -O--buildsystem=cmake debian/rules override_dh_fixperms-indep make[1]: Entering directory '/build/apbs-A5U5s9/apbs-3.4.1' dh_fixperms for example in FKBP/1d7h-dmso/UHBD/pqr2qcd \ ion-pmf/runme.sh \ point-pmf/runme.sh \ protein-rna/postprocess.sh \ protein-rna/test.sh \ helix/Run_membrane-helix.sh \ protein-rna/run_apdx_files.sh; \ do \ chmod +x debian/apbs-data/usr/share/apbs/examples/${example}; \ done for script in amber2charmm.sh \ param/pdb2pqr/amber2uhbd.sh \ qcd2pqr.awk; \ do \ chmod a+x debian/apbs-data/usr/share/apbs/tools/conversion/${script}; \ done for example in bem-pKa/test_proteins \ pbsam-barn_bars; \ do \ chmod a-x debian/apbs-data/usr/share/apbs/examples/${example}/*.pqr; \ done make[1]: Leaving directory '/build/apbs-A5U5s9/apbs-3.4.1' dh_missing -i -O--buildsystem=cmake dh_installdeb -i -O--buildsystem=cmake dh_gencontrol -i -O--buildsystem=cmake dpkg-gencontrol: warning: package apbs-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -i -O--buildsystem=cmake dh_builddeb -i -O--buildsystem=cmake dpkg-deb: building package 'apbs-data' in '../apbs-data_3.4.1-2_all.deb'. dpkg-deb: building package 'apbs-doc' in '../apbs-doc_3.4.1-2_all.deb'. dpkg-genbuildinfo --build=all -O../apbs_3.4.1-2_all.buildinfo dpkg-genchanges --build=all -O../apbs_3.4.1-2_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/apbs-A5U5s9 /tmp/apbs-3.4.1-2clh41mvc I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.CAmx4OZ2M0... I: success in 1278.6572 seconds md5: apbs-data_3.4.1-2_all.deb: OK md5: apbs-doc_3.4.1-2_all.deb: OK sha1: apbs-data_3.4.1-2_all.deb: OK sha1: apbs-doc_3.4.1-2_all.deb: OK sha256: apbs-data_3.4.1-2_all.deb: OK sha256: apbs-doc_3.4.1-2_all.deb: OK Checksums: OK