I: pbuilder: network access will be disabled during build I: Current time: Sun May 19 15:35:34 +14 2024 I: pbuilder-time-stamp: 1716082534 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [apbs_3.4.1-5.dsc] I: copying [./apbs_3.4.1.orig.tar.gz] I: copying [./apbs_3.4.1-5.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Jan 11 10:57:55 2023 +14 gpgv: using RSA key 9CA877749FAB2E4FA96862ECDC686A27B43481B0 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-5.dsc: no acceptable signature found dpkg-source: info: extracting apbs in apbs-3.4.1 dpkg-source: info: unpacking apbs_3.4.1.orig.tar.gz dpkg-source: info: unpacking apbs_3.4.1-5.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 dpkg-source: info: applying open-U-obsolete.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2894/tmp/hooks/D01_modify_environment starting debug: Running on codethink9-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 19 15:35 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2894/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2894/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2894 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.CfDqLBe3/pbuilderrc_89aK --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CfDqLBe3/b2 --logfile b2/build.log --extrapackages usrmerge apbs_3.4.1-5.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 18 06:48 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2894/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, pkg-config, libarpack2-dev, libmaloc-dev, libsuitesparse-dev, libsuperlu-dev, libtirpc-dev, mpi-default-dev, python3, python3-dev, python3-pybind11, python3-setuptools, python3-sphinx | sphinx, swig, zlib1g-dev, libjs-mathjax, python3-sphinx-rtd-theme, python3-yaml dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libarpack2-dev; however: Package libarpack2-dev is not installed. pbuilder-satisfydepends-dummy depends on libmaloc-dev; however: Package libmaloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libsuitesparse-dev; however: Package libsuitesparse-dev is not installed. pbuilder-satisfydepends-dummy depends on libsuperlu-dev; however: Package libsuperlu-dev is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx | sphinx; however: Package python3-sphinx is not installed. Package sphinx is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-yaml; however: Package python3-yaml is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-font-awesome{a} fonts-lato{a} fonts-mathjax{a} gettext{a} gettext-base{a} gfortran-12{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libamd2{a} libarchive-zip-perl{a} libarchive13{a} libarpack2{a} libarpack2-dev{a} libblas-dev{a} libblas3{a} libbrotli1{a} libbsd0{a} libbtf1{a} libcamd2{a} libcbor0.8{a} libccolamd2{a} libcholmod3{a} libcolamd2{a} libcurl4{a} libcxsparse3{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-12-dev{a} libgfortran5{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp25{a} libklu1{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libldl2{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmaloc-dev{a} libmaloc1{a} libmetis5{a} libmongoose2{a} libmunge2{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2{a} libproc2-0{a} libpsl5{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librbio2{a} librdmacm1{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsliplu1{a} libspqr2{a} libssh2-1{a} libsub-override-perl{a} libsuitesparse-dev{a} libsuitesparseconfig5{a} libsuperlu-dev{a} libsuperlu5{a} libtool{a} libuchardet0{a} libucx0{a} libumfpack5{a} libuv1{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} mpi-default-dev{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} pybind11-dev{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-build{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-importlib-metadata{a} python3-installer{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pep517{a} python3-pkg-resources{a} python3-pybind11{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-toml{a} python3-tomli{a} python3-tz{a} python3-urllib3{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} swig{a} swig4.0{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common libarchive-cpio-perl libcoarrays-openmpi-dev libeigen3-dev libgraphblas-dev libjson-xs-perl libldap-common libmail-sendmail-perl libpaper-utils libsasl2-modules lynx psmisc publicsuffix python3-numpy python3-pil wget xauth 0 packages upgraded, 202 newly installed, 0 to remove and 0 not upgraded. Need to get 100.0 MB of archives. After unpacking 454 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 fonts-lato all 2.0-2.1 [2696 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 12 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 sgml-base all 1.31 [15.4 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 libproc2-0 arm64 2:4.0.2-3 [60.1 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 procps arm64 2:4.0.2-3 [698 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 openssl arm64 3.0.8-1 [1373 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 ca-certificates all 20230311 [153 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 libedit2 arm64 3.1-20221030-2 [88.1 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 libcbor0.8 arm64 0.8.0-2+b1 [26.0 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libfido2-1 arm64 1.12.0-2+b1 [72.6 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 openssh-client arm64 1:9.2p1-2 [931 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 libarchive13 arm64 3.6.2-1 [316 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libcurl4 arm64 7.88.1-8 [361 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libjsoncpp25 arm64 1.9.5-4 [72.3 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 librhash0 arm64 1.4.3-3 [131 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libuv1 arm64 1.44.2-1 [133 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 cmake-data all 3.25.1-1 [2026 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 cmake arm64 3.25.1-1 [6806 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-2 [131 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 dh-python all 5.20230130 [104 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 xml-core all 0.18+nmu1 [23.8 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 docutils-common all 0.19+dfsg-6 [127 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 libgfortran-12-dev arm64 12.2.0-14 [396 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 gfortran-12 arm64 12.2.0-14 [8646 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 libnl-3-200 arm64 3.7.0-0.2+b1 [60.2 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 libnl-route-3-200 arm64 3.7.0-0.2+b1 [168 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 libibverbs1 arm64 44.0-2 [56.8 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 ibverbs-providers arm64 44.0-2 [306 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 libsuitesparseconfig5 arm64 1:5.12.0+dfsg-2 [23.8 kB] Get: 83 http://deb.debian.org/debian bookworm/main arm64 libamd2 arm64 1:5.12.0+dfsg-2 [33.8 kB] Get: 84 http://deb.debian.org/debian bookworm/main arm64 libblas3 arm64 3.11.0-2 [91.4 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB] Get: 86 http://deb.debian.org/debian bookworm/main arm64 libarpack2 arm64 3.8.0-3 [79.5 kB] Get: 87 http://deb.debian.org/debian bookworm/main arm64 libblas-dev arm64 3.11.0-2 [97.6 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 liblapack-dev arm64 3.11.0-2 [3065 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 libarpack2-dev arm64 3.8.0-3 [96.4 kB] Get: 90 http://deb.debian.org/debian bookworm/main arm64 libbtf1 arm64 1:5.12.0+dfsg-2 [25.2 kB] Get: 91 http://deb.debian.org/debian bookworm/main arm64 libcamd2 arm64 1:5.12.0+dfsg-2 [34.9 kB] Get: 92 http://deb.debian.org/debian bookworm/main arm64 libccolamd2 arm64 1:5.12.0+dfsg-2 [37.6 kB] Get: 93 http://deb.debian.org/debian bookworm/main arm64 libcolamd2 arm64 1:5.12.0+dfsg-2 [31.8 kB] Get: 94 http://deb.debian.org/debian bookworm/main arm64 libmetis5 arm64 5.1.0.dfsg-7 [154 kB] Get: 95 http://deb.debian.org/debian bookworm/main arm64 libcholmod3 arm64 1:5.12.0+dfsg-2 [285 kB] Get: 96 http://deb.debian.org/debian bookworm/main arm64 libcxsparse3 arm64 1:5.12.0+dfsg-2 [73.4 kB] Get: 97 http://deb.debian.org/debian bookworm/main arm64 libevent-2.1-7 arm64 2.1.12-stable-8 [168 kB] Get: 98 http://deb.debian.org/debian bookworm/main arm64 libevent-core-2.1-7 arm64 2.1.12-stable-8 [124 kB] Get: 99 http://deb.debian.org/debian bookworm/main arm64 libevent-extra-2.1-7 arm64 2.1.12-stable-8 [101 kB] Get: 100 http://deb.debian.org/debian bookworm/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-8 [53.7 kB] Get: 101 http://deb.debian.org/debian bookworm/main arm64 libevent-openssl-2.1-7 arm64 2.1.12-stable-8 [59.7 kB] Get: 102 http://deb.debian.org/debian bookworm/main arm64 libevent-dev arm64 2.1.12-stable-8 [302 kB] Get: 103 http://deb.debian.org/debian bookworm/main arm64 libexpat1-dev arm64 2.5.0-1 [135 kB] Get: 104 http://deb.debian.org/debian bookworm/main arm64 librdmacm1 arm64 44.0-2 [64.9 kB] Get: 105 http://deb.debian.org/debian bookworm/main arm64 libfabric1 arm64 1.17.0-3 [476 kB] Get: 106 http://deb.debian.org/debian bookworm/main arm64 libhwloc15 arm64 2.9.0-1 [133 kB] Get: 107 http://deb.debian.org/debian bookworm/main arm64 libnuma1 arm64 2.0.16-1 [20.3 kB] Get: 108 http://deb.debian.org/debian bookworm/main arm64 libnuma-dev arm64 2.0.16-1 [36.0 kB] Get: 109 http://deb.debian.org/debian bookworm/main arm64 libltdl7 arm64 2.4.7-5 [392 kB] Get: 110 http://deb.debian.org/debian bookworm/main arm64 libltdl-dev arm64 2.4.7-5 [165 kB] Get: 111 http://deb.debian.org/debian bookworm/main arm64 libhwloc-dev arm64 2.9.0-1 [734 kB] Get: 112 http://deb.debian.org/debian bookworm/main arm64 libpciaccess0 arm64 0.17-2 [50.4 kB] Get: 113 http://deb.debian.org/debian bookworm/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 114 http://deb.debian.org/debian bookworm/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 115 http://deb.debian.org/debian bookworm/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 116 http://deb.debian.org/debian bookworm/main arm64 libx11-data all 2:1.8.4-2 [292 kB] Get: 117 http://deb.debian.org/debian bookworm/main arm64 libx11-6 arm64 2:1.8.4-2 [736 kB] Get: 118 http://deb.debian.org/debian bookworm/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 119 http://deb.debian.org/debian bookworm/main arm64 libxnvctrl0 arm64 525.85.05-1 [13.3 kB] Get: 120 http://deb.debian.org/debian bookworm/main arm64 ocl-icd-libopencl1 arm64 2.3.1-1 [42.1 kB] Get: 121 http://deb.debian.org/debian bookworm/main arm64 libhwloc-plugins arm64 2.9.0-1 [17.2 kB] Get: 122 http://deb.debian.org/debian bookworm/main arm64 libnl-3-dev arm64 3.7.0-0.2+b1 [104 kB] Get: 123 http://deb.debian.org/debian bookworm/main arm64 libnl-route-3-dev arm64 3.7.0-0.2+b1 [200 kB] Get: 124 http://deb.debian.org/debian bookworm/main arm64 libibverbs-dev arm64 44.0-2 [613 kB] Get: 125 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 126 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 127 http://deb.debian.org/debian bookworm/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 128 http://deb.debian.org/debian bookworm/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 129 http://deb.debian.org/debian bookworm/main arm64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 130 http://deb.debian.org/debian bookworm/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 131 http://deb.debian.org/debian bookworm/main arm64 libklu1 arm64 1:5.12.0+dfsg-2 [77.1 kB] Get: 132 http://deb.debian.org/debian bookworm/main arm64 libldl2 arm64 1:5.12.0+dfsg-2 [24.8 kB] Get: 133 http://deb.debian.org/debian bookworm/main arm64 libmaloc1 arm64 1.5-1 [79.0 kB] Get: 134 http://deb.debian.org/debian bookworm/main arm64 libmaloc-dev arm64 1.5-1 [109 kB] Get: 135 http://deb.debian.org/debian bookworm/main arm64 libmongoose2 arm64 1:5.12.0+dfsg-2 [44.3 kB] Get: 136 http://deb.debian.org/debian bookworm/main arm64 libmunge2 arm64 0.5.15-2 [18.8 kB] Get: 137 http://deb.debian.org/debian bookworm/main arm64 libpmix2 arm64 4.2.2-1+b1 [554 kB] Get: 138 http://deb.debian.org/debian bookworm/main arm64 libucx0 arm64 1.13.1-1 [734 kB] Get: 139 http://deb.debian.org/debian bookworm/main arm64 libopenmpi3 arm64 4.1.4-3+b1 [2161 kB] Get: 140 http://deb.debian.org/debian bookworm/main arm64 openmpi-common all 4.1.4-3 [167 kB] Get: 141 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 142 http://deb.debian.org/debian bookworm/main arm64 libpmix-dev arm64 4.2.2-1+b1 [883 kB] Get: 143 http://deb.debian.org/debian bookworm/main arm64 openmpi-bin arm64 4.1.4-3+b1 [225 kB] Get: 144 http://deb.debian.org/debian bookworm/main arm64 libopenmpi-dev arm64 4.1.4-3+b1 [970 kB] Get: 145 http://deb.debian.org/debian bookworm/main arm64 libpkgconf3 arm64 1.8.1-1 [35.3 kB] Get: 146 http://deb.debian.org/debian bookworm/main arm64 libpython3.11 arm64 3.11.2-6 [1841 kB] Get: 147 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-dev arm64 3.11.2-6 [4395 kB] Get: 148 http://deb.debian.org/debian bookworm/main arm64 libpython3-dev arm64 3.11.2-1+b1 [9564 B] Get: 149 http://deb.debian.org/debian bookworm/main arm64 librbio2 arm64 1:5.12.0+dfsg-2 [38.9 kB] Get: 150 http://deb.debian.org/debian bookworm/main arm64 libsliplu1 arm64 1:5.12.0+dfsg-2 [46.6 kB] Get: 151 http://deb.debian.org/debian bookworm/main arm64 libspqr2 arm64 1:5.12.0+dfsg-2 [75.1 kB] Get: 152 http://deb.debian.org/debian bookworm/main arm64 libumfpack5 arm64 1:5.12.0+dfsg-2 [201 kB] Get: 153 http://deb.debian.org/debian bookworm/main arm64 libsuitesparse-dev arm64 1:5.12.0+dfsg-2 [885 kB] Get: 154 http://deb.debian.org/debian bookworm/main arm64 libsuperlu5 arm64 5.3.0+dfsg1-2+b1 [141 kB] Get: 155 http://deb.debian.org/debian bookworm/main arm64 libsuperlu-dev arm64 5.3.0+dfsg1-2+b1 [22.4 kB] Get: 156 http://deb.debian.org/debian bookworm/main arm64 libyaml-0-2 arm64 0.2.5-1 [50.4 kB] Get: 157 http://deb.debian.org/debian bookworm/main arm64 mpi-default-dev arm64 1.14 [5548 B] Get: 158 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB] Get: 159 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 160 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] Get: 161 http://deb.debian.org/debian bookworm/main arm64 pybind11-dev all 2.10.3-1 [186 kB] Get: 162 http://deb.debian.org/debian bookworm/main arm64 python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 163 http://deb.debian.org/debian bookworm/main arm64 python3-zipp all 1.0.0-6 [6696 B] Get: 164 http://deb.debian.org/debian bookworm/main arm64 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get: 165 http://deb.debian.org/debian bookworm/main arm64 python3-packaging all 23.0-1 [32.5 kB] Get: 166 http://deb.debian.org/debian bookworm/main arm64 python3-tomli all 2.0.1-2 [17.9 kB] Get: 167 http://deb.debian.org/debian bookworm/main arm64 python3-pep517 all 0.13.0-2 [17.4 kB] Get: 168 http://deb.debian.org/debian bookworm/main arm64 python3-toml all 0.10.2-1 [16.2 kB] Get: 169 http://deb.debian.org/debian bookworm/main arm64 python3-wheel all 0.38.4-1 [30.8 kB] Get: 170 http://deb.debian.org/debian bookworm/main arm64 python3-build all 0.9.0-1 [20.7 kB] Get: 171 http://deb.debian.org/debian bookworm/main arm64 python3-installer all 0.6.0+dfsg1-1 [18.1 kB] Get: 172 http://deb.debian.org/debian bookworm/main arm64 pybuild-plugin-pyproject all 5.20230130 [9092 B] Get: 173 http://deb.debian.org/debian bookworm/main arm64 python-babel-localedata all 2.10.3-1 [5615 kB] Get: 174 http://deb.debian.org/debian bookworm/main arm64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 175 http://deb.debian.org/debian bookworm/main arm64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 176 http://deb.debian.org/debian bookworm/main arm64 python3-tz all 2022.7.1-3 [30.1 kB] Get: 177 http://deb.debian.org/debian bookworm/main arm64 python3-babel all 2.10.3-1 [103 kB] Get: 178 http://deb.debian.org/debian bookworm/main arm64 python3-certifi all 2022.9.24-1 [153 kB] Get: 179 http://deb.debian.org/debian bookworm/main arm64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 180 http://deb.debian.org/debian bookworm/main arm64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 181 http://deb.debian.org/debian bookworm/main arm64 python3.11-dev arm64 3.11.2-6 [617 kB] Get: 182 http://deb.debian.org/debian bookworm/main arm64 python3-dev arm64 3.11.2-1+b1 [26.2 kB] Get: 183 http://deb.debian.org/debian bookworm/main arm64 python3-roman all 3.3-3 [9880 B] Get: 184 http://deb.debian.org/debian bookworm/main arm64 python3-docutils all 0.19+dfsg-6 [382 kB] Get: 185 http://deb.debian.org/debian bookworm/main arm64 python3-idna all 3.3-1 [39.4 kB] Get: 186 http://deb.debian.org/debian bookworm/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 187 http://deb.debian.org/debian bookworm/main arm64 python3-markupsafe arm64 2.1.2-1+b1 [13.3 kB] Get: 188 http://deb.debian.org/debian bookworm/main arm64 python3-jinja2 all 3.1.2-1 [119 kB] Get: 189 http://deb.debian.org/debian bookworm/main arm64 python3-pybind11 all 2.10.3-1 [199 kB] Get: 190 http://deb.debian.org/debian bookworm/main arm64 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get: 191 http://deb.debian.org/debian bookworm/main arm64 python3-six all 1.16.0-4 [17.5 kB] Get: 192 http://deb.debian.org/debian bookworm/main arm64 python3-urllib3 all 1.26.12-1 [117 kB] Get: 193 http://deb.debian.org/debian bookworm/main arm64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 194 http://deb.debian.org/debian bookworm/main arm64 python3-setuptools all 66.1.1-1 [521 kB] Get: 195 http://deb.debian.org/debian bookworm/main arm64 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 196 http://deb.debian.org/debian bookworm/main arm64 sphinx-common all 5.3.0-4 [653 kB] Get: 197 http://deb.debian.org/debian bookworm/main arm64 python3-sphinx all 5.3.0-4 [549 kB] Get: 198 http://deb.debian.org/debian bookworm/main arm64 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB] Get: 199 http://deb.debian.org/debian bookworm/main arm64 python3-sphinx-rtd-theme all 1.2.0+dfsg-1 [27.7 kB] Get: 200 http://deb.debian.org/debian bookworm/main arm64 python3-yaml arm64 6.0-3+b2 [108 kB] Get: 201 http://deb.debian.org/debian bookworm/main arm64 swig4.0 arm64 4.1.0-0.2 [1299 kB] Get: 202 http://deb.debian.org/debian bookworm/main arm64 swig all 4.1.0-0.2 [321 kB] Fetched 100.0 MB in 5s (22.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package fonts-lato. (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 ... 19616 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.0-2.1_all.deb ... Unpacking fonts-lato (2.0-2.1) ... Selecting previously unselected package libpython3.11-minimal:arm64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (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 ... 19958 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (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 ... 20392 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_arm64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../002-libproc2-0_2%3a4.0.2-3_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.2-3_arm64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.0.8-1_arm64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../008-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../011-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../014-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.11.2-2_arm64.deb ... 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Unpacking libopenmpi-dev:arm64 (4.1.4-3+b1) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../133-libpkgconf3_1.8.1-1_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-1) ... Selecting previously unselected package libpython3.11:arm64. Preparing to unpack .../134-libpython3.11_3.11.2-6_arm64.deb ... Unpacking libpython3.11:arm64 (3.11.2-6) ... Selecting previously unselected package libpython3.11-dev:arm64. Preparing to unpack .../135-libpython3.11-dev_3.11.2-6_arm64.deb ... Unpacking libpython3.11-dev:arm64 (3.11.2-6) ... Selecting previously unselected package libpython3-dev:arm64. Preparing to unpack .../136-libpython3-dev_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-dev:arm64 (3.11.2-1+b1) ... Selecting previously unselected package librbio2:arm64. Preparing to unpack .../137-librbio2_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking librbio2:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package libsliplu1:arm64. 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Unpacking python3-pygments (2.14.0+dfsg-1) ... Selecting previously unselected package python3-six. Preparing to unpack .../179-python3-six_1.16.0-4_all.deb ... Unpacking python3-six (1.16.0-4) ... Selecting previously unselected package python3-urllib3. Preparing to unpack .../180-python3-urllib3_1.26.12-1_all.deb ... Unpacking python3-urllib3 (1.26.12-1) ... Selecting previously unselected package python3-requests. Preparing to unpack .../181-python3-requests_2.28.1+dfsg-1_all.deb ... Unpacking python3-requests (2.28.1+dfsg-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../182-python3-setuptools_66.1.1-1_all.deb ... Unpacking python3-setuptools (66.1.1-1) ... Selecting previously unselected package python3-snowballstemmer. Preparing to unpack .../183-python3-snowballstemmer_2.2.0-2_all.deb ... Unpacking python3-snowballstemmer (2.2.0-2) ... Selecting previously unselected package sphinx-common. 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Preparing to unpack .../190-swig_4.1.0-0.2_all.deb ... Unpacking swig (4.1.0-0.2) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libpciaccess0:arm64 (0.17-2) ... Setting up libxau6:arm64 (1:1.0.9-1) ... Setting up libpsl5:arm64 (0.21.2-1) ... Setting up fonts-lato (2.0-2.1) ... Setting up fonts-mathjax (2.7.9+dfsg-1) ... Setting up libicu72:arm64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libjs-mathjax (2.7.9+dfsg-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-1) ... Setting up libcbor0.8:arm64 (0.8.0-2+b1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b6) ... Setting up libldl2:arm64 (1:5.12.0+dfsg-2) ... Setting up libnghttp2-14:arm64 (1.52.0-1) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libmetis5:arm64 (5.1.0.dfsg-7) ... Setting up file (1:5.44-3) ... Setting up pybind11-dev (2.10.3-1) ... Setting up libbtf1:arm64 (1:5.12.0+dfsg-2) ... Setting up python-babel-localedata (2.10.3-1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libpkgconf3:arm64 (1.8.1-1) ... Setting up libuv1:arm64 (1.44.2-1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libexpat1-dev:arm64 (2.5.0-1) ... Setting up libx11-data (2:1.8.4-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libproc2-0:arm64 (2:4.0.2-3) ... Setting up libhwloc15:arm64 (2.9.0-1) ... Setting up libevent-core-2.1-7:arm64 (2.1.12-stable-8) ... Setting up libevent-2.1-7:arm64 (2.1.12-stable-8) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:arm64 (1.9.5-4) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libltdl7:arm64 (2.4.7-5) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ... Setting up libgfortran5:arm64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up libnuma1:arm64 (2.0.16-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:arm64 (2.3.1-1) ... Setting up librhash0:arm64 (1.4.3-3) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libjson-perl (4.10000-1) ... Setting up libnl-3-200:arm64 (3.7.0-0.2+b1) ... Setting up openmpi-common (4.1.4-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:arm64 (1.10.0-3+b1) ... Setting up sgml-base (1.31) ... Setting up libcxsparse3:arm64 (1:5.12.0+dfsg-2) ... Setting up cmake-data (3.25.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up swig4.0 (4.1.0-0.2) ... Setting up libfido2-1:arm64 (1.12.0-2+b1) ... Setting up openssl (3.0.8-1) ... Setting up libbsd0:arm64 (0.11.7-2) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (1.2.0+dfsg-1) ... Setting up libsuitesparseconfig5:arm64 (1:5.12.0+dfsg-2) ... Setting up libblas-dev:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up librbio2:arm64 (1:5.12.0+dfsg-2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-8) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libamd2:arm64 (1:5.12.0+dfsg-2) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:arm64 (2.1.12-stable-8) ... Setting up liblapack3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up swig (4.1.0-0.2) ... Setting up libcolamd2:arm64 (1:5.12.0+dfsg-2) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:arm64 (3.6.2-1) ... Setting up libedit2:arm64 (3.1-20221030-2) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libarpack2:arm64 (3.8.0-3) ... Setting up libsuperlu5:arm64 (5.3.0+dfsg1-2+b1) ... Setting up libevent-openssl-2.1-7:arm64 (2.1.12-stable-8) ... Setting up libgfortran-12-dev:arm64 (12.2.0-14) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up pkgconf:arm64 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:arm64 (2.0.16-1) ... Setting up libnl-route-3-200:arm64 (3.7.0-0.2+b1) ... Setting up libsliplu1:arm64 (1:5.12.0+dfsg-2) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:arm64 (2.4.7-5) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libcamd2:arm64 (1:5.12.0+dfsg-2) ... Setting up libmongoose2:arm64 (1:5.12.0+dfsg-2) ... Setting up gfortran-12 (12.2.0-14) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libevent-dev (2.1.12-stable-8) ... Setting up liblapack-dev:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up pkg-config:arm64 (1.8.1-1) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libnl-3-dev:arm64 (3.7.0-0.2+b1) ... Setting up groff-base (1.22.4-10) ... Setting up libklu1:arm64 (1:5.12.0+dfsg-2) ... Setting up libccolamd2:arm64 (1:5.12.0+dfsg-2) ... Setting up xml-core (0.18+nmu1) ... Setting up libcurl4:arm64 (7.88.1-8) ... Setting up libx11-6:arm64 (2:1.8.4-2) ... Setting up libhwloc-dev:arm64 (2.9.0-1) ... Setting up libsuperlu-dev:arm64 (5.3.0+dfsg1-2+b1) ... Setting up libcholmod3:arm64 (1:5.12.0+dfsg-2) ... Setting up libmaloc1 (1.5-1) ... Setting up libspqr2:arm64 (1:5.12.0+dfsg-2) ... Setting up libibverbs1:arm64 (44.0-2) ... Setting up libarpack2-dev:arm64 (3.8.0-3) ... Setting up ibverbs-providers:arm64 (44.0-2) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:arm64 (525.85.05-1) ... Setting up libnl-route-3-dev:arm64 (3.7.0-0.2+b1) ... Setting up libumfpack5:arm64 (1:5.12.0+dfsg-2) ... Setting up sphinx-common (5.3.0-4) ... Setting up cmake (3.25.1-1) ... Setting up libmaloc-dev (1.5-1) ... Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up librdmacm1:arm64 (44.0-2) ... Setting up python3.11 (3.11.2-6) ... Setting up libucx0:arm64 (1.13.1-1) ... Setting up libpython3.11:arm64 (3.11.2-6) ... Setting up libsuitesparse-dev:arm64 (1:5.12.0+dfsg-2) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libibverbs-dev:arm64 (44.0-2) ... Setting up libhwloc-plugins:arm64 (2.9.0-1) ... Setting up python3-markupsafe (2.1.2-1+b1) ... Setting up python3-tz (2022.7.1-3) ... Setting up python3-six (1.16.0-4) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up python3-packaging (23.0-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-snowballstemmer (2.2.0-2) ... Setting up libpython3.11-dev:arm64 (3.11.2-6) ... Setting up python3-idna (3.3-1) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.6.0+dfsg1-1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-pybind11 (2.10.3-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-2) ... Setting up dh-python (5.20230130) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up libfabric1:arm64 (1.17.0-3) ... Setting up libpython3-dev:arm64 (3.11.2-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-tomli (2.0.1-2) ... Setting up libpmix2:arm64 (4.2.2-1+b1) ... Setting up python3-babel (2.10.3-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3.11-dev (3.11.2-6) ... Setting up python3-charset-normalizer (3.0.1-2) ... Setting up python3-alabaster (0.7.12-1) ... Setting up libopenmpi3:arm64 (4.1.4-3+b1) ... Setting up python3-yaml (6.0-3+b2) ... Setting up python3-zipp (1.0.0-6) ... Setting up python3-wheel (0.38.4-1) ... Setting up python3-pygments (2.14.0+dfsg-1) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up libpmix-dev:arm64 (4.2.2-1+b1) ... Setting up openmpi-bin (4.1.4-3+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up python3-importlib-metadata (4.12.0-1) ... Setting up python3-pep517 (0.13.0-2) ... Setting up libopenmpi-dev:arm64 (4.1.4-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Setting up python3-build (0.9.0-1) ... Setting up pybuild-plugin-pyproject (5.20230130) ... Setting up mpi-default-dev (1.14) ... Processing triggers for libc-bin (2.36-8) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.19+dfsg-6) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.19+dfsg-6) ... Setting up python3-sphinx (5.3.0-4) ... Setting up python3-sphinx-rtd-theme (1.2.0+dfsg-1) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). fakeroot is already the newest version (1.31-1.2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/2894/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... I: user script /srv/workspace/pbuilder/2894/tmp/hooks/A99_set_merged_usr finished hostname: Temporary failure in name resolution I: Running cd /build/apbs-3.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../apbs_3.4.1-5_source.changes dpkg-buildpackage: info: source package apbs dpkg-buildpackage: info: source version 3.4.1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael Banck dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 dh build --with python3,sphinxdoc --buildsystem=cmake dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/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-3.4.1/debian/external_deps/fetk \ -DRPC_CFLAGS=-I/usr/include/tirpc \ -DBUILD_MALOC=Off cd obj-aarch64-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 -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-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-3.4.1/debian/external_deps/fetk -DRPC_CFLAGS=-I/usr/include/tirpc -DBUILD_MALOC=Off .. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- 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 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-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/aarch64-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-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-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/aarch64-linux-gnu/libblas.so;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- Found LAPACK: /usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/aarch64-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/aarch64-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/aarch64-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/aarch64-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/aarch64-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/aarch64-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/aarch64-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/aarch64-linux-gnu/librt.a -- Adding librt: /usr/lib/aarch64-linux-gnu/librt.a 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-3.4.1/obj-aarch64-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: 2023-01-11T10:56:38 -- ** CURRENT_YEAR: 2023 -- 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/aarch64-linux-gnu/libblas.so;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/aarch64-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/aarch64-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/aarch64-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/aarch64-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/aarch64-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/aarch64-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/aarch64-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/aarch64-linux-gnu/librt.a -- Adding librt: /usr/lib/aarch64-linux-gnu/librt.a 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/aarch64-linux-gnu/libumfpack.so -- SUITESPARSE_INCLUDE_DIRS: /usr/include/suitesparse -- SUITESPARSE_LIBRARIES: /usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a -- Checking for MPI -- Found MPI_C: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/aarch64-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++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-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++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-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++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-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++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-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++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-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++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-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-3.4.1=. -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 "4.1.0") -- Found Python3: /usr/bin/python3 (found suitable version "3.11.2", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- ***** Python3 include path is: /usr/include/python3.11 -- ***** Python3 library path is: /usr/lib/aarch64-linux-gnu/libpython3.11.so -- ***** Python3 library dir is: /usr/lib/aarch64-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:180 (include) /usr/lib/cmake/pybind11/pybind11Config.cmake:248 (include) tools/python-pybind/CMakeLists.txt:2 (find_package) -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.11.2", minimum required is "3.6") -- Found PythonLibs: /usr/lib/aarch64-linux-gnu/libpython3.11.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/include (found version "2.10.3") -- LIBS mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-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 (found suitable exact version "3.11.2") found components: Interpreter -- ******* FOUND TEST CASE born, born -- TEST born_test WORKING_DIRECTORY /build/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/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-3.4.1/tests COMMAND /usr/bin/python3 /build/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-3.4.1/tests COMMAND /usr/bin/python3 /build/apbs-3.4.1/tests/apbs_tester.py -e apbs -t alkanes -- ******* FOUND TEST CASE FKBP, FKBP -- TEST FKBP_test WORKING_DIRECTORY /build/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/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-3.4.1/tests COMMAND /usr/bin/python3 /build/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-3.4.1/tests COMMAND /usr/bin/python3 /build/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-3.4.1/tests COMMAND /usr/bin/python3 /build/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-3.4.1/tests COMMAND /usr/bin/python3 /build/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-3.4.1/tests COMMAND /usr/bin/python3 /build/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-3.4.1/tests COMMAND /usr/bin/python3 /build/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-3.4.1/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/apbs-3.4.1' dh_auto_build -O--buildsystem=cmake cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/apbs-3.4.1 -B/build/apbs-3.4.1/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/apbs-3.4.1/obj-aarch64-linux-gnu/CMakeFiles /build/apbs-3.4.1/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/apbs-3.4.1/obj-aarch64-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[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/depend cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/DependInfo.cmake --color= make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/depend make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/DependInfo.cmake --color= 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-3.4.1/obj-aarch64-linux-gnu' cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/debian/external_deps/fetk/gamer/src /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/tools/python /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-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 make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build.make _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build Dependee "/build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake" is newer than depender "/build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend.internal". Dependee "/build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend.internal". make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' Scanning dependencies of target apbslib_swig_compilation make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/build make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [ 0%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77vers.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/f77vers.c [ 2%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i77vers.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i77vers.c [ 2%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scg.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scg.c [ 2%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgdrv.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgdrv.c [ 3%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/base/gamer_base.c.o [ 3%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/triangle/triangle.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/gamer/src/base/gamer_base.c [ 3%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scr.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scr.c [ 3%] Swig compile apbslib.i for python cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python && /usr/bin/cmake -E make_directory /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/gamer/src/triangle/triangle.c [ 3%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_rnge.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_rnge.c cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python && /usr/bin/cmake -E touch /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON.stamp [ 3%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/abort_.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/abort_.c cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python && /usr/bin/cmake -E env SWIG_LIB=/usr/share/swig4.0 /usr/bin/swig4.0 -python -outdir /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python -interface _apbslib -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/python3.11 -I/build/apbs-3.4.1/tools/python -o /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c /build/apbs-3.4.1/tools/python/apbslib.i [ 3%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/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-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/predicates.cpp [ 3%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/exit_.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/exit_.c [ 3%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scrind.c.o [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getarg_.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scrind.c cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/getarg_.c [ 5%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcg.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcg.c [ 5%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iargc_.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/iargc_.c [ 5%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgnr.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgnr.c [ 5%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getenv_.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/getenv_.c [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/signal_.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/signal_.c [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_stop.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_stop.c [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_paus.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_paus.c [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgne.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgne.c [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgnr.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgnr.c [ 7%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgne.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgne.c [ 7%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/system_.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/system_.c [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/cabs.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/cabs.c make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [ 8%] Built target apbslib_swig_compilation [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derf_.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/derf_.c [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/derfc_.c [ 8%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sppcg.c [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erfc_.c.o [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erf_.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/erfc_.c cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/erf_.c [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sig_die.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sig_die.c [ 9%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgca.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgca.c [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uninit.c.o [ 9%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sdpchb.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sdpchb.c cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/uninit.c cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/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-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ci.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ci.c [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_dd.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_dd.c [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_di.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_di.c [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_hh.c [ 11%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sckchb.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sckchb.c [ 11%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scbfix.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scbfix.c [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ii.c [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ri.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ri.c [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zi.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_zi.c [ 12%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgchk.c [ 13%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o [ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zz.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_zz.c cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sonest.c [ 15%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/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-3.4.1/debian/external_deps/fetk/gamer/src/biom/CorrectNormals.C [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_abs.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_abs.c [ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/msstop.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/msstop.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_cos.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_cos.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_div.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_div.c [ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/r1mach.c [ 16%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o [ 16%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sratqr.c [ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_exp.c cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgdrv.c [ 17%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcg.c [ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_log.c [ 17%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcr.c [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcrind.c [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_sin.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sqrt.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_sqrt.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_abs.c [ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcg.c [ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgnr.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgnr.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_cos.c [ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgne.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_div.c [ 20%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgnr.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgnr.c /build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function 'void tetgenmesh::constrainedfacets()': /build/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-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-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-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 *"); | ^~~~~~~~~ [ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_exp.c [ 21%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgne.c [ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_log.c /build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function 'long int tetgenmesh::reconstructmesh()': /build/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"); | ^~~~~ [ 21%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dppcg.c [ 22%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgca.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgca.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o cd 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-I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/ddpchb.c [ 22%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/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-3.4.1/debian/external_deps/fetk/gamer/src/biom/GenerateSphereMesh.C [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_sqrt.c [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o [ 23%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcbfix.c cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_abs.c [ 23%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o cd 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-I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgchk.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_acos.c [ 24%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/donest.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o [ 24%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_asin.c cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/mdstop.c [ 25%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/d1mach.c [ 25%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dratqr.c [ 25%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depsln.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/cgcode/depsln.c [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_atan.c [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atn2.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_atn2.c [ 26%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/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-3.4.1/debian/external_deps/fetk/gamer/src/biom/MarchingCube.C [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cnjg.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cos.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cos.c [ 28%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/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-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Mesh.C [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cosh.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cosh.c [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_dim.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_dim.c [ 28%] Linking C shared library libcgcode.so cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1=. -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 [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_exp.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_exp.c cd /build/apbs-3.4.1/obj-aarch64-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 make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_imag.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_imag.c [ 29%] Built target cgcode [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_int.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_int.c [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_lg10.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_lg10.c [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_log.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_log.c [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_mod.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_mod.c [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_nint.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_nint.c [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sign.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sign.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sin.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sin.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sinh.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sinh.c [ 31%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/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-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sqrt.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sqrt.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tan.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_tan.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tanh.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_tanh.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_abs.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_acos.c [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_asin.c [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atan.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_atan.c [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atn2.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_atn2.c [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cnjg.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cos.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cosh.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_dim.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_dim.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_exp.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_exp.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_imag.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_int.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_int.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_lg10.c [ 35%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadLattice.C.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/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-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadLattice.C [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_log.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_log.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_mod.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_mod.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_nint.c /build/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-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-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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_prod.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_prod.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sign.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sign.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sin.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sin.c [ 37%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/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-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadPDB.C [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sinh.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sinh.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sqrt.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_tan.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_tanh.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_abs.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_dim.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_dnnt.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_indx.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_len.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_len.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_mod.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_mod.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_nint.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_nint.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_sign.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_sign.c [ 42%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/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-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitbits.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lbitbits.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitshft.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lbitshft.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_abs.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_abs.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dim.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_dim.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dnnt.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_dnnt.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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_len.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_len.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_mod.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_mod.c [ 44%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/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-3.4.1/debian/external_deps/fetk/gamer/src/biom/RegionGrowing.C [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_nint.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_sign.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_ge.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_gt.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_le.c [ 45%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/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-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfaceMesh.C [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_lt.c /build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function 'SurfaceMesh* SurfaceMesh_readOFF(char*)': /build/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-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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 47%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/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-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfExtract.C /build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function 'GemMesh* GemMesh_fromSurfaceMesh(SurfaceMesh*, char*)': /build/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-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-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-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-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"); | ^~~~~~~~ [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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/ef1asc_.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ef1asc_.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1cmc_.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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/f77_aloc.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/f77_aloc.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cat.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_copy.c [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dtime_.c.o cd 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-ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/etime_.c [ 50%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/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-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfRefine.C [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/backspac.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c [ 50%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfSmooth.C.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/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-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfSmooth.C /build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c: In function 'f_back': /build/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/close.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/close.c [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dfe.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lwrite.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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/rdfmt.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rdfmt.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sue.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/typesize.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uio.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/uio.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/util.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/util.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wref.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsfe.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsle.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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/wsne.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsne.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/xwsne.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/punc/src/vf2c/main.c /build/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-3.4.1/obj-aarch64-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-3.4.1=. 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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-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-linux-gnu' cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/debian/external_deps/fetk/punc/src /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/CMakeFiles/punc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build.make 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_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-3.4.1/debian/external_deps/fetk/punc/src/base/punc_base.c [ 60%] Linking C shared library libpunc.so cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1=. -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/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so vf2c/libvf2c.so.1.9.3 cgcode/libcgcode.so.1.9.3 cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-linux-gnu' cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/debian/external_deps/fetk/mc/src /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src/CMakeFiles/mc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-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 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-I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c [ 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/bsolv.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/base/mc_base.c [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mat.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec.c [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matcopy.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/bam/mat.c cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/bam/matcopy.c [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matln.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/bam/mtool.c /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c: In function 'Bmat_ctor': /build/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-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-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:906, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bmat.h:121, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat_p.h:37, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:34: In function 'sprintf', inlined from 'Bmat_ctor' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:17: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 22 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_bcg': /build/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:906, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bvec.h:41, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec_p.h:37, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:34: In function 'sprintf', inlined from 'Bvec_bcg' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:922:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 9 and 88 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_bcg': /build/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 function 'sprintf', inlined from 'Bvec_bcg' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:919:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 13 and 92 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c: In function 'Bmat_galerkin': /build/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-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:32: note: directive argument in the range [0, 2147483646] 1018 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:32: note: directive argument in the range [0, 2147483646] In function 'sprintf', inlined from 'Bmat_galerkin' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:17: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 31 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cg': /build/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 function 'sprintf', inlined from 'Bvec_cg' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:631:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 87 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cg': /build/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 function 'sprintf', inlined from 'Bvec_cg' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:628:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 12 and 91 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/slu.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/bam/slu.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/bam/vec.c /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cgnr': /build/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 function 'sprintf', inlined from 'Bvec_cgnr' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1422:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 89 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cgnr': /build/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 function 'sprintf', inlined from 'Bvec_cgnr' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1419:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 14 and 93 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec3.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hcg': /build/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:906, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb_p.h:37, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:34: In function 'sprintf', inlined from 'Bvec_hcg' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:267:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 9 and 88 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hcg': /build/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 function 'sprintf', inlined from 'Bvec_hcg' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:264:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 13 and 92 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/whb/rcmat.c /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c: In function 'Bvec_ctorPoint': /build/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-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:24: note: directive argument in the range [0, 2147483646] 291 | sprintf(bname, "%s_%d", thee->name, p); | ^~~~~~~ In file included from /usr/include/stdio.h:906, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools_p.h:37, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:34: In function 'sprintf', inlined from 'Bvec_ctorPoint' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 21 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hbcg': /build/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 function 'sprintf', inlined from 'Bvec_hbcg' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:474:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 89 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hbcg': /build/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 function 'sprintf', inlined from 'Bvec_hbcg' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:471:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 14 and 93 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/brcmat.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/assem.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/aprx/assem.c [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/aprx.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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/bnode.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/aprx/estim.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/eval.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/aprx/io.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/node.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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/parti.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/aprx/parti.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/re.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/aprx/re.c /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function 'Aprx_fe2fd': /build/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:906, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:40, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/aprx_p.h:37, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:34: In function 'sprintf', inlined from 'Aprx_fe2fd' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:368:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function 'Aprx_fe2fd': /build/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 function 'sprintf', inlined from 'Aprx_fe2fd' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:366:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function 'Aprx_fe2fd': /build/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 function 'sprintf', inlined from 'Aprx_fe2fd' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:364:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/vel.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/gem/vel.c /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/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:906, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt_p.h:37, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:39: In function 'sprintf', inlined from 'Bvec_sfpcg' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:495:9, inlined from 'Bvec_submethod' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 11 and 90 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/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 function 'sprintf', inlined from 'Bvec_sfpcg' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:492:9, inlined from 'Bvec_submethod' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 15 and 94 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/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 function 'sprintf', inlined from 'Bvec_sfpbcg' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:776:9, inlined from 'Bvec_submethod' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 12 and 91 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/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 function 'sprintf', inlined from 'Bvec_sfpbcg' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:773:9, inlined from 'Bvec_submethod' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 95 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/ves.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/gem/gemio.c /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c: In function 'Gem_delaunay': /build/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-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: note: referencing argument 8 of type 'double *[4]' In file included from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:34: /build/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-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-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: note: referencing argument 8 of type 'double *[4]' /build/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-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-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: note: referencing argument 8 of type 'double *[4]' /build/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, | ^~~~~~~~~~~ [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemref.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/nam/lsolv.c /build/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-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: note: referencing argument 8 of type 'double *[4]' /build/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-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-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: note: referencing argument 8 of type 'double *[4]' /build/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-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-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: note: referencing argument 8 of type 'double *[4]' /build/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-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-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: note: referencing argument 8 of type 'double *[4]' /build/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-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-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: note: referencing argument 8 of type 'double *[4]' /build/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-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-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: note: referencing argument 8 of type 'double *[4]' /build/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, | ^~~~~~~~~~~ [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/nsolv.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-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-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/dyn/svio.c [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/mcsh/mcsh.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function 'Gem_writeTEC': /build/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:906, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:41, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:34: In function 'sprintf', inlined from 'Gem_writeTEC' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function 'Gem_writeTEC': /build/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 function 'sprintf', inlined from 'Gem_writeTEC' at /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 12 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c: In function 'MCsh_builtIn': /build/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-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: note: referencing argument 8 of type 'double *[4]' In file included from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:42, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/mc/am.h:43, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/mc/nam.h:36, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mc/mcsh.h:42, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh_p.h:37, from /build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:34: /build/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-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-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: note: referencing argument 8 of type 'double *[4]' /build/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-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-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: note: referencing argument 8 of type 'double *[4]' /build/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-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-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: note: referencing argument 8 of type 'double *[4]' /build/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-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-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: note: referencing argument 8 of type 'double *[4]' /build/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-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-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: note: referencing argument 8 of type 'double *[4]' /build/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, | ^~~~~~~~~~~~~ [ 73%] Linking C shared library libmc.so cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1=. -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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a -lmaloc ../../punc/src/libpunc.so.1.9.3 /usr/lib/aarch64-linux-gnu/libblas.so -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../punc/src/vf2c/libvf2c.so.1.9.3 ../../punc/src/cgcode/libcgcode.so.1.9.3 cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-linux-gnu' [ 73%] Built target mc make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/depend make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/depend cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/src/generic 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-I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/generic/femparm.c [ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/generic/pbamparm.c cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base 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-I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/pmgc/buildGd.c [ 76%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/generic/bemparm.c [ 77%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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 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-I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/generic/geoflowparm.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/generic/apolparm.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/generic/vacc.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/generic/valist.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/generic/vatom.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base 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-I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/generic/vclist.c [ 80%] Building C object 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-I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/generic/vstring.c [ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS 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-I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/generic/vparam.c [ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/generic/vgreen.c [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/pmgc/cgd.c [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/pmgc/gsd.c [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/pmgc/matvecd.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/pmgc/mgcsd.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/pmgc/mgdrvd.c [ 82%] Linking C shared library libapbs_generic.so cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1=. -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++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libblas.so [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/pmgc/mgsubd.c cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-linux-gnu' [ 82%] Built target apbs_generic make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/depend make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/src/fem /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem/CMakeFiles/apbs_fem.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-linux-gnu' [ 82%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/fem/vcsm.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/pmgc/mikpckd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/pmgc/mlinpckd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/pmgc/mypdec.c [ 84%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vfetk.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/fem/vfetk.c [ 84%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/pmgc/newtond.c [ 85%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/pmgc/newdrvd.c [ 85%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/pmgc/powerd.c /build/apbs-3.4.1/src/fem/vfetk.c: In function 'Vfetk_PDE_ctor2': /build/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; | ^ [ 85%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/pmgc/smoothd.c [ 85%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/pmgc/mgfasd.c [ 85%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vpee.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/fem/vpee.c /build/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/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:906, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-3.4.1/src/fem/vfetk.h:67, from /build/apbs-3.4.1/src/fem/vfetk.c:57: In function 'sprintf', inlined from 'Bmat_printHB' at /build/apbs-3.4.1/src/fem/vfetk.c:1073:5: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 6 and 18 bytes into a destination of size 17 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/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-3.4.1/src/fem/vfetk.c:1074:23: note: directive argument in the range [-2147483646, 2147483647] 1074 | sprintf(ptrfmtstr,"%%%dd",numZdigits+1); | ^~~~~~~ In function 'sprintf', inlined from 'Bmat_printHB' at /build/apbs-3.4.1/src/fem/vfetk.c:1074:5: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 14 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/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 function 'sprintf', inlined from 'Bmat_printHB' at /build/apbs-3.4.1/src/fem/vfetk.c:1075:5: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 6 and 18 bytes into a destination of size 17 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/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-3.4.1/src/fem/vfetk.c:1076:23: note: directive argument in the range [-2147483646, 2147483647] 1076 | sprintf(indfmtstr,"%%%dd",nrowdigits+1); | ^~~~~~~ In function 'sprintf', inlined from 'Bmat_printHB' at /build/apbs-3.4.1/src/fem/vfetk.c:1076:5: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 14 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 85%] Linking C shared library libapbs_fem.so cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1=. -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++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-linux-gnu' [ 85%] Built target apbs_fem [ 86%] Linking C shared library libapbs_pmgc.so cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1=. -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++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libblas.so cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-linux-gnu' cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/src/mg /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-linux-gnu' [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/mg/vgrid.c [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/mg/vmgrid.c [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/mg/vopot.c [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/mg/vpmgp.c [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/mg/vpmg.c /build/apbs-3.4.1/src/mg/vgrid.c: In function 'Vgrid_readDXBIN': /build/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-3.4.1/obj-aarch64-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-3.4.1=. -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++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 87%] Linking CXX shared library libgamer.so cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gamer.dir/link.txt --verbose=1 cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cmake -E cmake_symlink_library libapbs_mg.so.3 libapbs_mg.so.3 libapbs_mg.so /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/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 make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-linux-gnu' cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/src /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/src /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/build make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [ 87%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cc -Dapbs_routines_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/src/routines.c cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-linux-gnu' [ 87%] Built target gamer /build/apbs-3.4.1/src/routines.c: In function 'initAPOL': /build/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-3.4.1/src/routines.c:5046:20: note: referencing argument 2 of type 'char[1024]' /build/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-3.4.1/src/routines.c:5046:20: note: referencing argument 3 of type 'char[1024]' In file included from /build/apbs-3.4.1/src/generic/apolparm.h:73, from /build/apbs-3.4.1/src/generic/nosh.h:73, from /build/apbs-3.4.1/src/apbs.h:70, from /build/apbs-3.4.1/src/routines.h:64, from /build/apbs-3.4.1/src/routines.c:54: /build/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-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-3.4.1/src/routines.c:5048:24: note: referencing argument 2 of type 'char[1024]' /build/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-3.4.1/src/routines.c:5048:24: note: referencing argument 3 of type 'char[1024]' /build/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-3.4.1/src/routines.c: In function 'writematMG': /build/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:906, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-3.4.1/src/apbs.h:67: In function 'sprintf', inlined from 'writematMG' at /build/apbs-3.4.1/src/routines.c:2020:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/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 function 'sprintf', inlined from 'writedataMG' at /build/apbs-3.4.1/src/routines.c:2937:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 6 and 1029 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/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 function 'sprintf', inlined from 'writedataMG' at /build/apbs-3.4.1/src/routines.c:2963:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/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 function 'sprintf', inlined from 'writedataMG' at /build/apbs-3.4.1/src/routines.c:2919:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/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 function 'sprintf', inlined from 'writedataMG' at /build/apbs-3.4.1/src/routines.c:2954:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/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 function 'sprintf', inlined from 'writedataMG' at /build/apbs-3.4.1/src/routines.c:2944:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/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 function 'sprintf', inlined from 'writedataMG' at /build/apbs-3.4.1/src/routines.c:2930:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/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 function 'sprintf', inlined from 'writedataMG' at /build/apbs-3.4.1/src/routines.c:2909:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/src/routines.c: In function 'writedataFE': /build/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 function 'sprintf', inlined from 'writedataFE' at /build/apbs-3.4.1/src/routines.c:4893:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/src/routines.c: In function 'writedataFE': /build/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 function 'sprintf', inlined from 'writedataFE' at /build/apbs-3.4.1/src/routines.c:4887:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/src/routines.c: In function 'writedataFE': /build/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 function 'sprintf', inlined from 'writedataFE' at /build/apbs-3.4.1/src/routines.c:4880:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/src/routines.c: In function 'initAPOL': /build/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-3.4.1/src/routines.c:5046:20: note: referencing argument 2 of type 'char[1024]' /build/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-3.4.1/src/routines.c:5046:20: note: referencing argument 3 of type 'char[1024]' /build/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-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-3.4.1/src/routines.c:5048:24: note: referencing argument 2 of type 'char[1024]' /build/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-3.4.1/src/routines.c:5048:24: note: referencing argument 3 of type 'char[1024]' /build/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-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-3.4.1/src/routines.c:5046:20: note: referencing argument 2 of type 'char[1024]' /build/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-3.4.1/src/routines.c:5046:20: note: referencing argument 3 of type 'char[1024]' /build/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-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-3.4.1/src/routines.c:5048:24: note: referencing argument 2 of type 'char[1024]' /build/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-3.4.1/src/routines.c:5048:24: note: referencing argument 3 of type 'char[1024]' /build/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-3.4.1/obj-aarch64-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-3.4.1=. -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++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-linux-gnu' [ 88%] Built target apbs_routines make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/depend make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/src /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/src /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/CMakeFiles/apbs.dir/DependInfo.cmake --color= 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[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/tools/mesh /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/mgmesh.dir/DependInfo.cmake --color= make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/depend make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/tools/mesh /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/smooth.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/tools/mesh /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh 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-I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src 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-I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/tools/mesh/mergedx2.c [ 91%] Building C object tools/mesh/CMakeFiles/value.dir/value.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/tools/mesh/value.c /build/apbs-3.4.1/src/main.c: In function 'main': /build/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-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-3.4.1/obj-aarch64-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-3.4.1=. -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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 91%] Linking C executable ../bin/value cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1=. -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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 92%] Linking C executable ../bin/multivalue cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1=. -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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 92%] Linking C executable ../bin/smooth cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/smooth.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 92%] Linking C executable ../bin/dxmath cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dxmath.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 92%] Built target value make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/depend make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/tools/mesh /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/benchmark.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/build make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [ 92%] Built target 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-I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/tools/mesh/benchmark.c make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.dir/build make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [ 92%] Building C object tools/mesh/CMakeFiles/similarity.dir/similarity.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include 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-Wl,--no-as-needed CMakeFiles/apbs.dir/main.c.o -o apbs -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 92%] Building C object tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base 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-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-3.4.1/tools/mesh/dx2mol.c make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/build make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [ 92%] Linking C executable ../bin/mergedx cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx.dir/link.txt --verbose=1 [ 92%] Building C object tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/tools/mesh/dx2uhbd.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 93%] Linking C executable ../bin/benchmark cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 93%] Linking C executable ../bin/mergedx2 cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx2.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [ 94%] Linking C executable ../bin/dx2uhbd cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script 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../../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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make 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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-3.4.1/tools/mesh/tensor2dx.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [ 96%] Built target benchmark make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/depend [ 96%] Built target mergedx2 make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/tools/mesh 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/build/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c [ 97%] Building C object tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/tools/manip/coulomb.c /build/apbs-3.4.1/tools/mesh/tensor2dx.c: In function 'main': /build/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-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-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-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-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-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-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-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-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-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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-3.4.1/tools/mesh/del2dx.c: In function 'main': /build/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-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-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-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-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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [ 98%] Linking C executable ../bin/similarity cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/similarity.dir/link.txt --verbose=1 [ 98%] Built target dx2mol make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/depend make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-3.4.1 /build/apbs-3.4.1/tools/manip /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip/CMakeFiles/born.dir/DependInfo.cmake --color= [ 98%] Built target dx2uhbd make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/python/CMakeFiles/_apbslib.dir/build.make 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-I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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-3.4.1/tools/manip/born.c make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-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-3.4.1/obj-aarch64-linux-gnu' [ 98%] Linking C executable ../bin/tensor2dx cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script 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-I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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 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/usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 98%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/module.cpp.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/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-3.4.1/tools/python-pybind/module.cpp /build/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c: In function 'main': /build/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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 99%] Linking C executable ../bin/del2dx cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/del2dx.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 99%] Linking C executable ../bin/uhbd_asc2bin cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/uhbd_asc2bin.dir/link.txt --verbose=1 [ 99%] Linking C executable ../bin/coulomb cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1=. -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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [ 99%] Built target similarity [ 99%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/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-3.4.1/tools/python-pybind/bind_nosh.cpp make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [ 99%] Built target tensor2dx [100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/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-3.4.1/tools/python-pybind/bind_vatom.cpp make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Built target del2dx [100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/apbs-3.4.1/src -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/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-3.4.1/tools/python-pybind/bind_valist.cpp make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Linking C executable ../bin/born cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/born.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Built target uhbd_asc2bin /usr/bin/cc -g -O2 -ffile-prefix-map=/build/apbs-3.4.1=. -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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [100%] Built target coulomb make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Built target born [100%] Linking C shared library _apbslib.so cd /build/apbs-3.4.1/obj-aarch64-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-3.4.1=. -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++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../src/libapbs_routines.so.3 /usr/lib/aarch64-linux-gnu/libpython3.11.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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Built target _apbslib [100%] Linking CXX shared module apbs.cpython-311-aarch64-linux-gnu.so cd /build/apbs-3.4.1/obj-aarch64-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-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-311-aarch64-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++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-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/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Built target apbs_pybind make[2]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/apbs-3.4.1/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' debian/rules execute_after_dh_auto_build-indep make[1]: Entering directory '/build/apbs-3.4.1' PYTHONPATH=/build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python sphinx-build -b html docs /build/apbs-3.4.1/obj-aarch64-linux-gnu/docs/_build/html # HTML generator Running Sphinx v5.3.0 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 Failed to import apbs.input_file.calculate.boundary_element. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' Failed to import apbs.input_file. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' Failed to import apbs.input_file.process. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' Failed to import apbs.input_file.calculate.nonpolar.Nonpolar. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' Failed to import apbs.input_file.read. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' Failed to import apbs.input_file.calculate. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' Failed to import apbs.input_file.calculate.generic. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' Failed to import apbs.input_file.calculate.finite_difference. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' Failed to import apbs.input_file.calculate.finite_element. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' 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-3.4.1/docs/getting/index.rst:41: ERROR: Unexpected indentation. /build/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "geometric flow". /build/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "fetk". /build/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "pbam/pbsam". /build/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "tabi-pb". WARNING: autodoc: failed to import module 'input_file.calculate.boundary_element' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate.finite_difference' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate.finite_element' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate.generic' from module 'apbs'; the following exception was raised: No module named 'pyparsing' /build/apbs-3.4.1/docs/using/input/new/calculate/index.rst:33: ERROR: Document or section may not begin with a transition. /build/apbs-3.4.1/docs/using/input/new/calculate/index.rst:33: ERROR: Document may not end with a transition. WARNING: autodoc: failed to import module 'input_file.calculate.nonpolar.Nonpolar' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.process' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.read' from module 'apbs'; the following exception was raised: No module named 'pyparsing' looking for now-outdated files... none found pickling environment... done checking consistency... /build/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... 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[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, 19 warnings. The HTML pages are in obj-aarch64-linux-gnu/docs/_build/html. make[1]: Leaving directory '/build/apbs-3.4.1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=cmake dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_installdirs -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake cd obj-aarch64-linux-gnu && make -j8 install DESTDIR=/build/apbs-3.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/apbs-3.4.1 -B/build/apbs-3.4.1/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "RELWITHDEBINFO" -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindUMFPACK.cmake -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindSuperLU.cmake -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindSuiteSparse.cmake -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindLAPACK.cmake -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindARPACK.cmake -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindAMD.cmake -- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/punc/punc.h -- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/punc/punc_base.h -- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/punc/punccf.h -- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/punc/punc_base_p.h -- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libpunc.so.1.9.3 -- Installing: 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/build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/vparam -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/vparam/vparam-amber-parm94.xml -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/vparam/vparam-amber-parm94.dat -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/c-alpha.dat -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/weiner86-param.dat -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/amber2uhbd.sh -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/amber-param.dat -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/amber2charmm.sh -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/WHATIF2AMBER.sed -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/README.md -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/CMakeLists.txt -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/born -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/coulomb -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/uhbd_asc2bin -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/del2dx -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/tensor2dx -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/similarity -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/analysis -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/dx2mol -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/dx2uhbd -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/mergedx2 -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/benchmark -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/mergedx -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/dxmath -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/smooth -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/multivalue -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/value -- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/mgmesh make[1]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/apbs-3.4.1' (cd tests; PATH=/build/apbs-3.4.1/debian/tmp/usr/bin:${PATH} LD_LIBRARY_PATH=/build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu:${LD_LIBRARY_PATH} PYTHONPATH=${PYTHONPATH}:/build/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-3.4.1/build -------------------------------------------------------------------------------- Testing forces from apbs-forces.in Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.004373 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in CHECKING:/build/apbs-3.4.1/debian/tmp/usr/bin/apbs NOTE: Using apbs binary:/build/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-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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: 16.333126 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-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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: 12.571019 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-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE0.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE1.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE2.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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 = 8.142935605695E+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 8.142935605695e+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-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE3.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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) = -5.762728344953E+01 kJ/mol Global net ELEC energy = -5.762728344953E+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 -5.762728344953e+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: 65.84394 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, 3257.1427835730997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867462003] 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 3257.1427835730997 COMPUTED RESULT 5941.0039478710005 COMPUTED RESULT 1190.8714828309999 COMPUTED RESULT 3519.7218230368003 COMPUTED RESULT 6171.495796544 COMPUTED RESULT -230.49184867462003 BINARY: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE0.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE1.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE2.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE3.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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: 68.485394 seconds -------------------------------------------------------------------------------- Total elapsed time: 163.237852 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-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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) = 1.048683058621E+02 kJ/mol Global net ELEC energy = 1.048683058621E+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 (1.048683058621e+02, 1.048683060915e+02) *** PASSED *** Elapsed time: 511.423484 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, 104.8683058621] 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 104.8683058621 BINARY: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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) = 1.095841077688E+02 kJ/mol Global net ELEC energy = 1.095841077688E+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 (1.095841077688e+02, 1.095841074454e+02) *** PASSED *** Elapsed time: 389.191313 seconds -------------------------------------------------------------------------------- Total elapsed time: 900.614797 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, 109.5841077688] 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 109.5841077688 Running tests for alkanes section BINARY: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: alkanes.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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: 45.204524 seconds -------------------------------------------------------------------------------- Total elapsed time: 45.204524 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-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-mol.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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) = 1.500810086373E+01 kJ/mol Global net ELEC energy = 1.500810086373E+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 (1.500810086373e+01, 1.500810086371e+01) *** PASSED *** Elapsed time: 62.994971 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, 15.00810086373] 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 15.00810086373 BINARY: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-smol.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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) = 1.624454192074E+01 kJ/mol Global net ELEC energy = 1.624454192074E+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 (1.624454192074e+01, 1.624454192072e+01) *** PASSED *** Elapsed time: 52.434554 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, 16.24454192074] 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 16.24454192074 BINARY: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-mol.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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) = 1.442499933664E+01 kJ/mol Global net ELEC energy = 1.442499933664E+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 (1.442499933664e+01, 1.442500529301e+01) *** PASSED *** Elapsed time: 63.387122 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, 14.42499933664] 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 14.42499933664 BINARY: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-smol.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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) = 1.545150742843E+01 kJ/mol Global net ELEC energy = 1.545150742843E+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 (1.545150742843e+01, 1.545150009785e+01) *** PASSED *** Elapsed time: 55.997732 seconds -------------------------------------------------------------------------------- Total elapsed time: 234.814379 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, 15.45150742843] 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 15.45150742843 Running tests for hca-bind section BINARY: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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) = -5.246475812684E+01 kJ/mol Global net ELEC energy = -5.246475812684E+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 (-5.246475812684e+01, -5.246475812665e+01) *** PASSED *** Elapsed time: 61.306001 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, -52.46475812684] 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 -52.46475812684 BINARY: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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) = -5.405979017059E+01 kJ/mol Global net ELEC energy = -5.405979017059E+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 (-5.405979017059e+01, -5.405977880082e+01) *** PASSED *** Elapsed time: 47.286402 seconds -------------------------------------------------------------------------------- Total elapsed time: 108.592403 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, -54.05979017059] 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 -54.05979017059 Running tests for ionize section BINARY: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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: 36.283984 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-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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: 28.262008 seconds -------------------------------------------------------------------------------- Total elapsed time: 64.545992 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-3.4.1/debian/tmp/usr/bin/apbs INPUT: ion-pmf.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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 9.128e-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 -2.766e-05 tot 1 -2.723e-02 9.131e-07 9.134e-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 -2.768e-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: -6.909718345777E+00 WCA energy for atom 1: -6.909411348230E+00 Total WCA energy: -13.8191 kJ/mol Total non-polar energy = -1.365306965532E+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 8.398642197664E+01 -1.324564203755E-05 -1.613436083011E-05 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 0 6.148357059184E+00 -2.667517416421E-05 -5.378919663831E-05 tot 0 9.013477903582E+01 -3.992081620176E-05 -6.992355746842E-05 qf 1 -8.466423642736E+01 -1.836748085161E-05 -3.062224261564E-05 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 1 2.882739230549E+00 -3.149946352664E-05 -6.291495498709E-05 tot 1 -8.178149719681E+01 -4.986694437825E-05 -9.353719760273E-05 tot all 8.353281839012E+00 -8.978776058001E-05 -1.634607550711E-04 print APOL energy 1 (asolv) end Global net APOL energy = -1.365306965532E+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 -5.826577103767E-01 -2.766566538180E-05 -2.766098638935E-05 tot 0 -1.158042745371E+01 -2.766566538180E-05 -2.766098638935E-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 5.826650307914E-01 -2.767034437463E-05 -2.767796940038E-05 tot 1 1.170128938668E+01 -2.767034437463E-05 -2.767796940038E-05 tot all 1.208619329787E-01 -5.533600975643E-05 -5.533895578973E-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: 31.005433 seconds -------------------------------------------------------------------------------- Total elapsed time: 31.005433 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, -13.65306965532] EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] COMPUTED RESULT 7839.535983197 COMPUTED RESULT 8964.727588811 COMPUTED RESULT -1125.191605614 COMPUTED RESULT -13.65306965532 Running tests for pka-lig section BINARY: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-vdw.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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) = 8.083515648803E+00 kJ/mol Global net ELEC energy = 8.083515648803E+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 (8.083515648803e+00, 8.083515648730e+00) *** PASSED *** Elapsed time: 93.940642 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, 8.083515648803] 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 8.083515648803 BINARY: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-vdw.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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) = 2.096300255720E+01 kJ/mol Global net ELEC energy = 2.096300255720E+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 (2.096300255720e+01, 2.096296139195e+01) *** PASSED *** Elapsed time: 67.266331 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, 20.9630025572] 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 20.9630025572 BINARY: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-surf.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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) = 1.192607686582E+02 kJ/mol Global net ELEC energy = 1.192607686582E+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 (1.192607686582e+02, 1.192608095265e+02) *** PASSED *** Elapsed time: 76.331912 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, 119.2607686582] 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 119.2607686582 BINARY: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-surf.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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: 62.802978 seconds -------------------------------------------------------------------------------- Total elapsed time: 300.341863 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-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_1.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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: 7.21277 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-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_2.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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) = 8.906694086751E+00 kJ/mol Global net ELEC energy = 8.906694086751E+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 (8.906694086751e+00, 8.906694086750e+00) *** PASSED *** Elapsed time: 6.977794 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, 8.906694086751] 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 8.906694086751 BINARY: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_3.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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: 7.809032 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-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_4.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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: 7.77269 seconds -------------------------------------------------------------------------------- Total elapsed time: 29.772286 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-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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) = -3.624863488075E+01 kJ/mol Global net ELEC energy = -3.624863488075E+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 (-3.624863488075e+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: 12.335631 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, -36.24863488075, -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 -36.24863488075 COMPUTED RESULT -390.4121708125 COMPUTED RESULT -354.1635359318 BINARY: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/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 Jan 10 2023 at 20:56:38 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) = -3.757593772492E+01 kJ/mol Global net ELEC energy = -3.757593772492E+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 (-3.757593772492e+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: 11.284035 seconds -------------------------------------------------------------------------------- Total elapsed time: 23.619666 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, -37.57593772492, -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 -37.57593772492 COMPUTED RESULT -391.2388603848 COMPUTED RESULT -353.6629226599 make[1]: Leaving directory '/build/apbs-3.4.1' dh_install -O--buildsystem=cmake dh_installdocs -O--buildsystem=cmake dh_sphinxdoc -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake dh_installman -O--buildsystem=cmake dh_python3 -O--buildsystem=cmake I: dh_python3 fs:483: renaming _apbslib.so to _apbslib.cpython-311-aarch64-linux-gnu.so dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake debian/rules override_dh_fixperms-indep make[1]: Entering directory '/build/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-3.4.1' dh_fixperms -O--buildsystem=cmake -Napbs-data -Napbs-doc dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dwz: debian/libapbs3/usr/lib/aarch64-linux-gnu/libapbs_pmgc.so.3: DWARF compression not beneficial - old size 156418 new size 157333 dwz: debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3: DWARF compression not beneficial - old size 90756 new size 93482 dwz: debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libmc.so.1.9.3: DWARF compression not beneficial - old size 456981 new size 462714 dwz: debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libgamer.so.1.9.3: DWARF compression not beneficial - old size 920429 new size 923848 dwz: debian/python3-apbslib/usr/lib/python3/dist-packages/apbs.cpython-311-aarch64-linux-gnu.so: DWARF compression not beneficial - old size 6124877 new size 6137165 dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: symbol atan2 used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol acos used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol erfc used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol asin used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sinh used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sincos used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sin used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol log used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol tanh used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol atan used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol log used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol pow_dd used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol dnrm2_ used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol ddot_ used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol scopy_ used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sdot_ used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol snrm2_ used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol pow_ri used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol cosh used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol dcopy_ used by debian/libfetk1.9/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libumfpack.so.5 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libarpack.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libccolamd.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libgomp.so.1 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libapbs_fem.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libpunc.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libapbs_pmgc.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libmpi.so.40 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libcgcode.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libcholmod.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libamd.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libsuperlu.so.5 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libcolamd.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libsuitesparseconfig.so.5 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libvf2c.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libcamd.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libstdc++.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libspqr.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libblas.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/bin/apbs were not linked against libmc.so.1.9 (they use none of the library's symbols) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: Depends field of package libapbs-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package apbs: substitution variable ${sphinxdoc:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libfetk-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package apbs: substitution variable ${sphinxdoc:Depends} used, but is not defined dpkg-gencontrol: warning: package apbs-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'libapbs3-dbgsym' in '../libapbs3-dbgsym_3.4.1-5_arm64.deb'. dpkg-deb: building package 'apbs' in '../apbs_3.4.1-5_arm64.deb'. dpkg-deb: building package 'libapbs-dev' in '../libapbs-dev_3.4.1-5_arm64.deb'. dpkg-deb: building package 'apbs-doc' in '../apbs-doc_3.4.1-5_all.deb'. dpkg-deb: building package 'libfetk1.9' in '../libfetk1.9_3.4.1-5_arm64.deb'. dpkg-deb: building package 'python3-apbslib' in '../python3-apbslib_3.4.1-5_arm64.deb'. dpkg-deb: building package 'apbs-dbgsym' in '../apbs-dbgsym_3.4.1-5_arm64.deb'. dpkg-deb: building package 'apbs-data' in '../apbs-data_3.4.1-5_all.deb'. dpkg-deb: building package 'libapbs3' in '../libapbs3_3.4.1-5_arm64.deb'. dpkg-deb: building package 'python3-apbslib-dbgsym' in '../python3-apbslib-dbgsym_3.4.1-5_arm64.deb'. dpkg-deb: building package 'libfetk1.9-dbgsym' in '../libfetk1.9-dbgsym_3.4.1-5_arm64.deb'. dpkg-deb: building package 'libfetk-dev' in '../libfetk-dev_3.4.1-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../apbs_3.4.1-5_arm64.buildinfo dpkg-genchanges --build=binary -O../apbs_3.4.1-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2894/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2894/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2894 and its subdirectories I: Current time: Sun May 19 16:15:21 +14 2024 I: pbuilder-time-stamp: 1716084921