I: pbuilder: network access will be disabled during build
I: Current time: Sun Apr 16 06:32:57 -12 2023
I: pbuilder-time-stamp: 1681669977
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 Tue Jan 10 08:57:55 2023 -12
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/17545/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8'
DISTRIBUTION='bookworm'
HOME='/var/lib/jenkins'
HOST_ARCH='arm64'
IFS='
'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='17545'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.CfDqLBe3/pbuilderrc_IDe8 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CfDqLBe3/b1 --logfile b1/build.log apbs_3.4.1-5.dsc'
SUDO_GID='117'
SUDO_UID='110'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
USERNAME='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.16:3128'
I: uname -a
Linux codethink10-arm64 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 Apr 14 00:48 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/17545/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 <pbuilder-maint@lists.alioth.debian.org>
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 3s (36.7 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 ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package libbsd0:arm64.
Preparing to unpack .../016-libbsd0_0.11.7-2_arm64.deb ...
Unpacking libbsd0:arm64 (0.11.7-2) ...
Selecting previously unselected package libedit2:arm64.
Preparing to unpack .../017-libedit2_3.1-20221030-2_arm64.deb ...
Unpacking libedit2:arm64 (3.1-20221030-2) ...
Selecting previously unselected package libcbor0.8:arm64.
Preparing to unpack .../018-libcbor0.8_0.8.0-2+b1_arm64.deb ...
Unpacking libcbor0.8:arm64 (0.8.0-2+b1) ...
Selecting previously unselected package libfido2-1:arm64.
Preparing to unpack .../019-libfido2-1_1.12.0-2+b1_arm64.deb ...
Unpacking libfido2-1:arm64 (1.12.0-2+b1) ...
Selecting previously unselected package openssh-client.
Preparing to unpack .../020-openssh-client_1%3a9.2p1-2_arm64.deb ...
Unpacking openssh-client (1:9.2p1-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../021-m4_1.4.19-3_arm64.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../022-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../023-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../024-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../025-autopoint_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package libicu72:arm64.
Preparing to unpack .../026-libicu72_72.1-3_arm64.deb ...
Unpacking libicu72:arm64 (72.1-3) ...
Selecting previously unselected package libxml2:arm64.
Preparing to unpack .../027-libxml2_2.9.14+dfsg-1.1+b3_arm64.deb ...
Unpacking libxml2:arm64 (2.9.14+dfsg-1.1+b3) ...
Selecting previously unselected package libarchive13:arm64.
Preparing to unpack .../028-libarchive13_3.6.2-1_arm64.deb ...
Unpacking libarchive13:arm64 (3.6.2-1) ...
Selecting previously unselected package libbrotli1:arm64.
Preparing to unpack .../029-libbrotli1_1.0.9-2+b6_arm64.deb ...
Unpacking libbrotli1:arm64 (1.0.9-2+b6) ...
Selecting previously unselected package libsasl2-modules-db:arm64.
Preparing to unpack .../030-libsasl2-modules-db_2.1.28+dfsg-10_arm64.deb ...
Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ...
Selecting previously unselected package libsasl2-2:arm64.
Preparing to unpack .../031-libsasl2-2_2.1.28+dfsg-10_arm64.deb ...
Unpacking libsasl2-2:arm64 (2.1.28+dfsg-10) ...
Selecting previously unselected package libldap-2.5-0:arm64.
Preparing to unpack .../032-libldap-2.5-0_2.5.13+dfsg-5_arm64.deb ...
Unpacking libldap-2.5-0:arm64 (2.5.13+dfsg-5) ...
Selecting previously unselected package libnghttp2-14:arm64.
Preparing to unpack .../033-libnghttp2-14_1.52.0-1_arm64.deb ...
Unpacking libnghttp2-14:arm64 (1.52.0-1) ...
Selecting previously unselected package libpsl5:arm64.
Preparing to unpack .../034-libpsl5_0.21.2-1_arm64.deb ...
Unpacking libpsl5:arm64 (0.21.2-1) ...
Selecting previously unselected package librtmp1:arm64.
Preparing to unpack .../035-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_arm64.deb ...
Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:arm64.
Preparing to unpack .../036-libssh2-1_1.10.0-3+b1_arm64.deb ...
Unpacking libssh2-1:arm64 (1.10.0-3+b1) ...
Selecting previously unselected package libcurl4:arm64.
Preparing to unpack .../037-libcurl4_7.88.1-8_arm64.deb ...
Unpacking libcurl4:arm64 (7.88.1-8) ...
Selecting previously unselected package libjsoncpp25:arm64.
Preparing to unpack .../038-libjsoncpp25_1.9.5-4_arm64.deb ...
Unpacking libjsoncpp25:arm64 (1.9.5-4) ...
Selecting previously unselected package librhash0:arm64.
Preparing to unpack .../039-librhash0_1.4.3-3_arm64.deb ...
Unpacking librhash0:arm64 (1.4.3-3) ...
Selecting previously unselected package libuv1:arm64.
Preparing to unpack .../040-libuv1_1.44.2-1_arm64.deb ...
Unpacking libuv1:arm64 (1.44.2-1) ...
Selecting previously unselected package cmake-data.
Preparing to unpack .../041-cmake-data_3.25.1-1_all.deb ...
Unpacking cmake-data (3.25.1-1) ...
Selecting previously unselected package cmake.
Preparing to unpack .../042-cmake_3.25.1-1_arm64.deb ...
Unpacking cmake (3.25.1-1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../043-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../044-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../045-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../046-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../047-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../048-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../049-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:arm64.
Preparing to unpack .../050-libelf1_0.188-2.1_arm64.deb ...
Unpacking libelf1:arm64 (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../051-dwz_0.15-1_arm64.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../052-gettext_0.21-12_arm64.deb ...
Unpacking gettext (0.21-12) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../053-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../054-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../055-debhelper_13.11.4_all.deb ...
Unpacking debhelper (13.11.4) ...
Selecting previously unselected package python3-lib2to3.
Preparing to unpack .../056-python3-lib2to3_3.11.2-2_all.deb ...
Unpacking python3-lib2to3 (3.11.2-2) ...
Selecting previously unselected package python3-distutils.
Preparing to unpack .../057-python3-distutils_3.11.2-2_all.deb ...
Unpacking python3-distutils (3.11.2-2) ...
Selecting previously unselected package dh-python.
Preparing to unpack .../058-dh-python_5.20230130_all.deb ...
Unpacking dh-python (5.20230130) ...
Selecting previously unselected package xml-core.
Preparing to unpack .../059-xml-core_0.18+nmu1_all.deb ...
Unpacking xml-core (0.18+nmu1) ...
Selecting previously unselected package docutils-common.
Preparing to unpack .../060-docutils-common_0.19+dfsg-6_all.deb ...
Unpacking docutils-common (0.19+dfsg-6) ...
Selecting previously unselected package fonts-font-awesome.
Preparing to unpack .../061-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ...
Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
Selecting previously unselected package fonts-mathjax.
Preparing to unpack .../062-fonts-mathjax_2.7.9+dfsg-1_all.deb ...
Unpacking fonts-mathjax (2.7.9+dfsg-1) ...
Selecting previously unselected package libgfortran5:arm64.
Preparing to unpack .../063-libgfortran5_12.2.0-14_arm64.deb ...
Unpacking libgfortran5:arm64 (12.2.0-14) ...
Selecting previously unselected package libgfortran-12-dev:arm64.
Preparing to unpack .../064-libgfortran-12-dev_12.2.0-14_arm64.deb ...
Unpacking libgfortran-12-dev:arm64 (12.2.0-14) ...
Selecting previously unselected package gfortran-12.
Preparing to unpack .../065-gfortran-12_12.2.0-14_arm64.deb ...
Unpacking gfortran-12 (12.2.0-14) ...
Selecting previously unselected package libnl-3-200:arm64.
Preparing to unpack .../066-libnl-3-200_3.7.0-0.2+b1_arm64.deb ...
Unpacking libnl-3-200:arm64 (3.7.0-0.2+b1) ...
Selecting previously unselected package libnl-route-3-200:arm64.
Preparing to unpack .../067-libnl-route-3-200_3.7.0-0.2+b1_arm64.deb ...
Unpacking libnl-route-3-200:arm64 (3.7.0-0.2+b1) ...
Selecting previously unselected package libibverbs1:arm64.
Preparing to unpack .../068-libibverbs1_44.0-2_arm64.deb ...
Unpacking libibverbs1:arm64 (44.0-2) ...
Selecting previously unselected package ibverbs-providers:arm64.
Preparing to unpack .../069-ibverbs-providers_44.0-2_arm64.deb ...
Unpacking ibverbs-providers:arm64 (44.0-2) ...
Selecting previously unselected package libsuitesparseconfig5:arm64.
Preparing to unpack .../070-libsuitesparseconfig5_1%3a5.12.0+dfsg-2_arm64.deb ...
Unpacking libsuitesparseconfig5:arm64 (1:5.12.0+dfsg-2) ...
Selecting previously unselected package libamd2:arm64.
Preparing to unpack .../071-libamd2_1%3a5.12.0+dfsg-2_arm64.deb ...
Unpacking libamd2:arm64 (1:5.12.0+dfsg-2) ...
Selecting previously unselected package libblas3:arm64.
Preparing to unpack .../072-libblas3_3.11.0-2_arm64.deb ...
Unpacking libblas3:arm64 (3.11.0-2) ...
Selecting previously unselected package liblapack3:arm64.
Preparing to unpack .../073-liblapack3_3.11.0-2_arm64.deb ...
Unpacking liblapack3:arm64 (3.11.0-2) ...
Selecting previously unselected package libarpack2:arm64.
Preparing to unpack .../074-libarpack2_3.8.0-3_arm64.deb ...
Unpacking libarpack2:arm64 (3.8.0-3) ...
Selecting previously unselected package libblas-dev:arm64.
Preparing to unpack .../075-libblas-dev_3.11.0-2_arm64.deb ...
Unpacking libblas-dev:arm64 (3.11.0-2) ...
Selecting previously unselected package liblapack-dev:arm64.
Preparing to unpack .../076-liblapack-dev_3.11.0-2_arm64.deb ...
Unpacking liblapack-dev:arm64 (3.11.0-2) ...
Selecting previously unselected package libarpack2-dev:arm64.
Preparing to unpack .../077-libarpack2-dev_3.8.0-3_arm64.deb ...
Unpacking libarpack2-dev:arm64 (3.8.0-3) ...
Selecting previously unselected package libbtf1:arm64.
Preparing to unpack .../078-libbtf1_1%3a5.12.0+dfsg-2_arm64.deb ...
Unpacking libbtf1:arm64 (1:5.12.0+dfsg-2) ...
Selecting previously unselected package libcamd2:arm64.
Preparing to unpack .../079-libcamd2_1%3a5.12.0+dfsg-2_arm64.deb ...
Unpacking libcamd2:arm64 (1:5.12.0+dfsg-2) ...
Selecting previously unselected package libccolamd2:arm64.
Preparing to unpack .../080-libccolamd2_1%3a5.12.0+dfsg-2_arm64.deb ...
Unpacking libccolamd2:arm64 (1:5.12.0+dfsg-2) ...
Selecting previously unselected package libcolamd2:arm64.
Preparing to unpack .../081-libcolamd2_1%3a5.12.0+dfsg-2_arm64.deb ...
Unpacking libcolamd2:arm64 (1:5.12.0+dfsg-2) ...
Selecting previously unselected package libmetis5:arm64.
Preparing to unpack .../082-libmetis5_5.1.0.dfsg-7_arm64.deb ...
Unpacking libmetis5:arm64 (5.1.0.dfsg-7) ...
Selecting previously unselected package libcholmod3:arm64.
Preparing to unpack .../083-libcholmod3_1%3a5.12.0+dfsg-2_arm64.deb ...
Unpacking libcholmod3:arm64 (1:5.12.0+dfsg-2) ...
Selecting previously unselected package libcxsparse3:arm64.
Preparing to unpack .../084-libcxsparse3_1%3a5.12.0+dfsg-2_arm64.deb ...
Unpacking libcxsparse3:arm64 (1:5.12.0+dfsg-2) ...
Selecting previously unselected package libevent-2.1-7:arm64.
Preparing to unpack .../085-libevent-2.1-7_2.1.12-stable-8_arm64.deb ...
Unpacking libevent-2.1-7:arm64 (2.1.12-stable-8) ...
Selecting previously unselected package libevent-core-2.1-7:arm64.
Preparing to unpack .../086-libevent-core-2.1-7_2.1.12-stable-8_arm64.deb ...
Unpacking libevent-core-2.1-7:arm64 (2.1.12-stable-8) ...
Selecting previously unselected package libevent-extra-2.1-7:arm64.
Preparing to unpack .../087-libevent-extra-2.1-7_2.1.12-stable-8_arm64.deb ...
Unpacking libevent-extra-2.1-7:arm64 (2.1.12-stable-8) ...
Selecting previously unselected package libevent-pthreads-2.1-7:arm64.
Preparing to unpack .../088-libevent-pthreads-2.1-7_2.1.12-stable-8_arm64.deb ...
Unpacking libevent-pthreads-2.1-7:arm64 (2.1.12-stable-8) ...
Selecting previously unselected package libevent-openssl-2.1-7:arm64.
Preparing to unpack .../089-libevent-openssl-2.1-7_2.1.12-stable-8_arm64.deb ...
Unpacking libevent-openssl-2.1-7:arm64 (2.1.12-stable-8) ...
Selecting previously unselected package libevent-dev.
Preparing to unpack .../090-libevent-dev_2.1.12-stable-8_arm64.deb ...
Unpacking libevent-dev (2.1.12-stable-8) ...
Selecting previously unselected package libexpat1-dev:arm64.
Preparing to unpack .../091-libexpat1-dev_2.5.0-1_arm64.deb ...
Unpacking libexpat1-dev:arm64 (2.5.0-1) ...
Selecting previously unselected package librdmacm1:arm64.
Preparing to unpack .../092-librdmacm1_44.0-2_arm64.deb ...
Unpacking librdmacm1:arm64 (44.0-2) ...
Selecting previously unselected package libfabric1:arm64.
Preparing to unpack .../093-libfabric1_1.17.0-3_arm64.deb ...
Unpacking libfabric1:arm64 (1.17.0-3) ...
Selecting previously unselected package libhwloc15:arm64.
Preparing to unpack .../094-libhwloc15_2.9.0-1_arm64.deb ...
Unpacking libhwloc15:arm64 (2.9.0-1) ...
Selecting previously unselected package libnuma1:arm64.
Preparing to unpack .../095-libnuma1_2.0.16-1_arm64.deb ...
Unpacking libnuma1:arm64 (2.0.16-1) ...
Selecting previously unselected package libnuma-dev:arm64.
Preparing to unpack .../096-libnuma-dev_2.0.16-1_arm64.deb ...
Unpacking libnuma-dev:arm64 (2.0.16-1) ...
Selecting previously unselected package libltdl7:arm64.
Preparing to unpack .../097-libltdl7_2.4.7-5_arm64.deb ...
Unpacking libltdl7:arm64 (2.4.7-5) ...
Selecting previously unselected package libltdl-dev:arm64.
Preparing to unpack .../098-libltdl-dev_2.4.7-5_arm64.deb ...
Unpacking libltdl-dev:arm64 (2.4.7-5) ...
Selecting previously unselected package libhwloc-dev:arm64.
Preparing to unpack .../099-libhwloc-dev_2.9.0-1_arm64.deb ...
Unpacking libhwloc-dev:arm64 (2.9.0-1) ...
Selecting previously unselected package libpciaccess0:arm64.
Preparing to unpack .../100-libpciaccess0_0.17-2_arm64.deb ...
Unpacking libpciaccess0:arm64 (0.17-2) ...
Selecting previously unselected package libxau6:arm64.
Preparing to unpack .../101-libxau6_1%3a1.0.9-1_arm64.deb ...
Unpacking libxau6:arm64 (1:1.0.9-1) ...
Selecting previously unselected package libxdmcp6:arm64.
Preparing to unpack .../102-libxdmcp6_1%3a1.1.2-3_arm64.deb ...
Unpacking libxdmcp6:arm64 (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:arm64.
Preparing to unpack .../103-libxcb1_1.15-1_arm64.deb ...
Unpacking libxcb1:arm64 (1.15-1) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../104-libx11-data_2%3a1.8.4-2_all.deb ...
Unpacking libx11-data (2:1.8.4-2) ...
Selecting previously unselected package libx11-6:arm64.
Preparing to unpack .../105-libx11-6_2%3a1.8.4-2_arm64.deb ...
Unpacking libx11-6:arm64 (2:1.8.4-2) ...
Selecting previously unselected package libxext6:arm64.
Preparing to unpack .../106-libxext6_2%3a1.3.4-1+b1_arm64.deb ...
Unpacking libxext6:arm64 (2:1.3.4-1+b1) ...
Selecting previously unselected package libxnvctrl0:arm64.
Preparing to unpack .../107-libxnvctrl0_525.85.05-1_arm64.deb ...
Unpacking libxnvctrl0:arm64 (525.85.05-1) ...
Selecting previously unselected package ocl-icd-libopencl1:arm64.
Preparing to unpack .../108-ocl-icd-libopencl1_2.3.1-1_arm64.deb ...
Unpacking ocl-icd-libopencl1:arm64 (2.3.1-1) ...
Selecting previously unselected package libhwloc-plugins:arm64.
Preparing to unpack .../109-libhwloc-plugins_2.9.0-1_arm64.deb ...
Unpacking libhwloc-plugins:arm64 (2.9.0-1) ...
Selecting previously unselected package libnl-3-dev:arm64.
Preparing to unpack .../110-libnl-3-dev_3.7.0-0.2+b1_arm64.deb ...
Unpacking libnl-3-dev:arm64 (3.7.0-0.2+b1) ...
Selecting previously unselected package libnl-route-3-dev:arm64.
Preparing to unpack .../111-libnl-route-3-dev_3.7.0-0.2+b1_arm64.deb ...
Unpacking libnl-route-3-dev:arm64 (3.7.0-0.2+b1) ...
Selecting previously unselected package libibverbs-dev:arm64.
Preparing to unpack .../112-libibverbs-dev_44.0-2_arm64.deb ...
Unpacking libibverbs-dev:arm64 (44.0-2) ...
Selecting previously unselected package libjs-jquery.
Preparing to unpack .../113-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Selecting previously unselected package libjs-jquery-ui.
Preparing to unpack .../114-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ...
Selecting previously unselected package libjs-mathjax.
Preparing to unpack .../115-libjs-mathjax_2.7.9+dfsg-1_all.deb ...
Unpacking libjs-mathjax (2.7.9+dfsg-1) ...
Selecting previously unselected package libjs-underscore.
Preparing to unpack .../116-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ...
Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
Selecting previously unselected package libjs-sphinxdoc.
Preparing to unpack .../117-libjs-sphinxdoc_5.3.0-4_all.deb ...
Unpacking libjs-sphinxdoc (5.3.0-4) ...
Selecting previously unselected package libjson-perl.
Preparing to unpack .../118-libjson-perl_4.10000-1_all.deb ...
Unpacking libjson-perl (4.10000-1) ...
Selecting previously unselected package libklu1:arm64.
Preparing to unpack .../119-libklu1_1%3a5.12.0+dfsg-2_arm64.deb ...
Unpacking libklu1:arm64 (1:5.12.0+dfsg-2) ...
Selecting previously unselected package libldl2:arm64.
Preparing to unpack .../120-libldl2_1%3a5.12.0+dfsg-2_arm64.deb ...
Unpacking libldl2:arm64 (1:5.12.0+dfsg-2) ...
Selecting previously unselected package libmaloc1.
Preparing to unpack .../121-libmaloc1_1.5-1_arm64.deb ...
Unpacking libmaloc1 (1.5-1) ...
Selecting previously unselected package libmaloc-dev.
Preparing to unpack .../122-libmaloc-dev_1.5-1_arm64.deb ...
Unpacking libmaloc-dev (1.5-1) ...
Selecting previously unselected package libmongoose2:arm64.
Preparing to unpack .../123-libmongoose2_1%3a5.12.0+dfsg-2_arm64.deb ...
Unpacking libmongoose2:arm64 (1:5.12.0+dfsg-2) ...
Selecting previously unselected package libmunge2.
Preparing to unpack .../124-libmunge2_0.5.15-2_arm64.deb ...
Unpacking libmunge2 (0.5.15-2) ...
Selecting previously unselected package libpmix2:arm64.
Preparing to unpack .../125-libpmix2_4.2.2-1+b1_arm64.deb ...
Unpacking libpmix2:arm64 (4.2.2-1+b1) ...
Selecting previously unselected package libucx0:arm64.
Preparing to unpack .../126-libucx0_1.13.1-1_arm64.deb ...
Unpacking libucx0:arm64 (1.13.1-1) ...
Selecting previously unselected package libopenmpi3:arm64.
Preparing to unpack .../127-libopenmpi3_4.1.4-3+b1_arm64.deb ...
Unpacking libopenmpi3:arm64 (4.1.4-3+b1) ...
Selecting previously unselected package openmpi-common.
Preparing to unpack .../128-openmpi-common_4.1.4-3_all.deb ...
Unpacking openmpi-common (4.1.4-3) ...
Selecting previously unselected package zlib1g-dev:arm64.
Preparing to unpack .../129-zlib1g-dev_1%3a1.2.13.dfsg-1_arm64.deb ...
Unpacking zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ...
Selecting previously unselected package libpmix-dev:arm64.
Preparing to unpack .../130-libpmix-dev_4.2.2-1+b1_arm64.deb ...
Unpacking libpmix-dev:arm64 (4.2.2-1+b1) ...
Selecting previously unselected package openmpi-bin.
Preparing to unpack .../131-openmpi-bin_4.1.4-3+b1_arm64.deb ...
Unpacking openmpi-bin (4.1.4-3+b1) ...
Selecting previously unselected package libopenmpi-dev:arm64.
Preparing to unpack .../132-libopenmpi-dev_4.1.4-3+b1_arm64.deb ...
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.
Preparing to unpack .../138-libsliplu1_1%3a5.12.0+dfsg-2_arm64.deb ...
Unpacking libsliplu1:arm64 (1:5.12.0+dfsg-2) ...
Selecting previously unselected package libspqr2:arm64.
Preparing to unpack .../139-libspqr2_1%3a5.12.0+dfsg-2_arm64.deb ...
Unpacking libspqr2:arm64 (1:5.12.0+dfsg-2) ...
Selecting previously unselected package libumfpack5:arm64.
Preparing to unpack .../140-libumfpack5_1%3a5.12.0+dfsg-2_arm64.deb ...
Unpacking libumfpack5:arm64 (1:5.12.0+dfsg-2) ...
Selecting previously unselected package libsuitesparse-dev:arm64.
Preparing to unpack .../141-libsuitesparse-dev_1%3a5.12.0+dfsg-2_arm64.deb ...
Unpacking libsuitesparse-dev:arm64 (1:5.12.0+dfsg-2) ...
Selecting previously unselected package libsuperlu5:arm64.
Preparing to unpack .../142-libsuperlu5_5.3.0+dfsg1-2+b1_arm64.deb ...
Unpacking libsuperlu5:arm64 (5.3.0+dfsg1-2+b1) ...
Selecting previously unselected package libsuperlu-dev:arm64.
Preparing to unpack .../143-libsuperlu-dev_5.3.0+dfsg1-2+b1_arm64.deb ...
Unpacking libsuperlu-dev:arm64 (5.3.0+dfsg1-2+b1) ...
Selecting previously unselected package libyaml-0-2:arm64.
Preparing to unpack .../144-libyaml-0-2_0.2.5-1_arm64.deb ...
Unpacking libyaml-0-2:arm64 (0.2.5-1) ...
Selecting previously unselected package mpi-default-dev.
Preparing to unpack .../145-mpi-default-dev_1.14_arm64.deb ...
Unpacking mpi-default-dev (1.14) ...
Selecting previously unselected package pkgconf-bin.
Preparing to unpack .../146-pkgconf-bin_1.8.1-1_arm64.deb ...
Unpacking pkgconf-bin (1.8.1-1) ...
Selecting previously unselected package pkgconf:arm64.
Preparing to unpack .../147-pkgconf_1.8.1-1_arm64.deb ...
Unpacking pkgconf:arm64 (1.8.1-1) ...
Selecting previously unselected package pkg-config:arm64.
Preparing to unpack .../148-pkg-config_1.8.1-1_arm64.deb ...
Unpacking pkg-config:arm64 (1.8.1-1) ...
Selecting previously unselected package pybind11-dev.
Preparing to unpack .../149-pybind11-dev_2.10.3-1_all.deb ...
Unpacking pybind11-dev (2.10.3-1) ...
Selecting previously unselected package python3-more-itertools.
Preparing to unpack .../150-python3-more-itertools_8.10.0-2_all.deb ...
Unpacking python3-more-itertools (8.10.0-2) ...
Selecting previously unselected package python3-zipp.
Preparing to unpack .../151-python3-zipp_1.0.0-6_all.deb ...
Unpacking python3-zipp (1.0.0-6) ...
Selecting previously unselected package python3-importlib-metadata.
Preparing to unpack .../152-python3-importlib-metadata_4.12.0-1_all.deb ...
Unpacking python3-importlib-metadata (4.12.0-1) ...
Selecting previously unselected package python3-packaging.
Preparing to unpack .../153-python3-packaging_23.0-1_all.deb ...
Unpacking python3-packaging (23.0-1) ...
Selecting previously unselected package python3-tomli.
Preparing to unpack .../154-python3-tomli_2.0.1-2_all.deb ...
Unpacking python3-tomli (2.0.1-2) ...
Selecting previously unselected package python3-pep517.
Preparing to unpack .../155-python3-pep517_0.13.0-2_all.deb ...
Unpacking python3-pep517 (0.13.0-2) ...
Selecting previously unselected package python3-toml.
Preparing to unpack .../156-python3-toml_0.10.2-1_all.deb ...
Unpacking python3-toml (0.10.2-1) ...
Selecting previously unselected package python3-wheel.
Preparing to unpack .../157-python3-wheel_0.38.4-1_all.deb ...
Unpacking python3-wheel (0.38.4-1) ...
Selecting previously unselected package python3-build.
Preparing to unpack .../158-python3-build_0.9.0-1_all.deb ...
Unpacking python3-build (0.9.0-1) ...
Selecting previously unselected package python3-installer.
Preparing to unpack .../159-python3-installer_0.6.0+dfsg1-1_all.deb ...
Unpacking python3-installer (0.6.0+dfsg1-1) ...
Selecting previously unselected package pybuild-plugin-pyproject.
Preparing to unpack .../160-pybuild-plugin-pyproject_5.20230130_all.deb ...
Unpacking pybuild-plugin-pyproject (5.20230130) ...
Selecting previously unselected package python-babel-localedata.
Preparing to unpack .../161-python-babel-localedata_2.10.3-1_all.deb ...
Unpacking python-babel-localedata (2.10.3-1) ...
Selecting previously unselected package python3-alabaster.
Preparing to unpack .../162-python3-alabaster_0.7.12-1_all.deb ...
Unpacking python3-alabaster (0.7.12-1) ...
Selecting previously unselected package python3-pkg-resources.
Preparing to unpack .../163-python3-pkg-resources_66.1.1-1_all.deb ...
Unpacking python3-pkg-resources (66.1.1-1) ...
Selecting previously unselected package python3-tz.
Preparing to unpack .../164-python3-tz_2022.7.1-3_all.deb ...
Unpacking python3-tz (2022.7.1-3) ...
Selecting previously unselected package python3-babel.
Preparing to unpack .../165-python3-babel_2.10.3-1_all.deb ...
Unpacking python3-babel (2.10.3-1) ...
Selecting previously unselected package python3-certifi.
Preparing to unpack .../166-python3-certifi_2022.9.24-1_all.deb ...
Unpacking python3-certifi (2022.9.24-1) ...
Selecting previously unselected package python3-chardet.
Preparing to unpack .../167-python3-chardet_5.1.0+dfsg-2_all.deb ...
Unpacking python3-chardet (5.1.0+dfsg-2) ...
Selecting previously unselected package python3-charset-normalizer.
Preparing to unpack .../168-python3-charset-normalizer_3.0.1-2_all.deb ...
Unpacking python3-charset-normalizer (3.0.1-2) ...
Selecting previously unselected package python3.11-dev.
Preparing to unpack .../169-python3.11-dev_3.11.2-6_arm64.deb ...
Unpacking python3.11-dev (3.11.2-6) ...
Selecting previously unselected package python3-dev.
Preparing to unpack .../170-python3-dev_3.11.2-1+b1_arm64.deb ...
Unpacking python3-dev (3.11.2-1+b1) ...
Selecting previously unselected package python3-roman.
Preparing to unpack .../171-python3-roman_3.3-3_all.deb ...
Unpacking python3-roman (3.3-3) ...
Selecting previously unselected package python3-docutils.
Preparing to unpack .../172-python3-docutils_0.19+dfsg-6_all.deb ...
Unpacking python3-docutils (0.19+dfsg-6) ...
Selecting previously unselected package python3-idna.
Preparing to unpack .../173-python3-idna_3.3-1_all.deb ...
Unpacking python3-idna (3.3-1) ...
Selecting previously unselected package python3-imagesize.
Preparing to unpack .../174-python3-imagesize_1.4.1-1_all.deb ...
Unpacking python3-imagesize (1.4.1-1) ...
Selecting previously unselected package python3-markupsafe.
Preparing to unpack .../175-python3-markupsafe_2.1.2-1+b1_arm64.deb ...
Unpacking python3-markupsafe (2.1.2-1+b1) ...
Selecting previously unselected package python3-jinja2.
Preparing to unpack .../176-python3-jinja2_3.1.2-1_all.deb ...
Unpacking python3-jinja2 (3.1.2-1) ...
Selecting previously unselected package python3-pybind11.
Preparing to unpack .../177-python3-pybind11_2.10.3-1_all.deb ...
Unpacking python3-pybind11 (2.10.3-1) ...
Selecting previously unselected package python3-pygments.
Preparing to unpack .../178-python3-pygments_2.14.0+dfsg-1_all.deb ...
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.
Preparing to unpack .../184-sphinx-common_5.3.0-4_all.deb ...
Unpacking sphinx-common (5.3.0-4) ...
Selecting previously unselected package python3-sphinx.
Preparing to unpack .../185-python3-sphinx_5.3.0-4_all.deb ...
Unpacking python3-sphinx (5.3.0-4) ...
Selecting previously unselected package sphinx-rtd-theme-common.
Preparing to unpack .../186-sphinx-rtd-theme-common_1.2.0+dfsg-1_all.deb ...
Unpacking sphinx-rtd-theme-common (1.2.0+dfsg-1) ...
Selecting previously unselected package python3-sphinx-rtd-theme.
Preparing to unpack .../187-python3-sphinx-rtd-theme_1.2.0+dfsg-1_all.deb ...
Unpacking python3-sphinx-rtd-theme (1.2.0+dfsg-1) ...
Selecting previously unselected package python3-yaml.
Preparing to unpack .../188-python3-yaml_6.0-3+b2_arm64.deb ...
Unpacking python3-yaml (6.0-3+b2) ...
Selecting previously unselected package swig4.0.
Preparing to unpack .../189-swig4.0_4.1.0-0.2_arm64.deb ...
Unpacking swig4.0 (4.1.0-0.2) ...
Selecting previously unselected package swig.
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...
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: Running cd /build/apbs-3.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-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 <mbanck@debian.org>
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: 2023-01-10T08:56:38
-- ** 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 -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.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/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=
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".
Scanning dependencies of target apbslib_swig_compilation
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]: 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[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
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/build
make[3]: Entering 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'
[ 0%] 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
[ 0%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scr.c.o
[ 1%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scg.c.o
[ 1%] 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/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
[ 1%] 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/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
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
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
[ 1%] 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
[ 2%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/base/gamer_base.c.o
[ 2%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scrind.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/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
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
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 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
[ 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/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
[ 4%] 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
[ 4%] 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
[ 4%] 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
[ 4%] 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
[ 4%] 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
[ 4%] 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
[ 5%] 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/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
[ 6%] 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
[ 6%] 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
[ 6%] 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
[ 7%] 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
[ 7%] 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
make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[ 7%] 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
[ 7%] Built target apbslib_swig_compilation
[ 8%] 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
[ 8%] 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
[ 8%] 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
[ 8%] 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
[ 8%] 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
[ 8%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o
[ 9%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.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/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
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
[ 9%] 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
[ 9%] 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
[ 9%] 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
[ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.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
[ 10%] 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/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
[ 10%] 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
[ 11%] 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
[ 11%] 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
[ 11%] 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
[ 11%] 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
[ 12%] 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/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
[ 13%] 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
[ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erfc_.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
[ 13%] 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
[ 13%] 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
[ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uninit.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/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
[ 13%] 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
[ 14%] 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
[ 14%] 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
[ 15%] 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
[ 15%] 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
[ 15%] 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
[ 15%] 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
[ 15%] 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
[ 16%] 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
[ 16%] 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
[ 16%] 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
[ 17%] 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
[ 17%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/ddpchb.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/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
[ 17%] 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
[ 17%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o
[ 18%] 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/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/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
[ 18%] 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
[ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o
[ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgchk.c.o
[ 19%] 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/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/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
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
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/dckchb.c.o -MF CMakeFiles/cgcode.dir/dckchb.c.o.d -o CMakeFiles/cgcode.dir/dckchb.c.o -c /build/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dckchb.c
[ 19%] 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
[ 20%] 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
[ 20%] 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
[ 20%] 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
[ 20%] 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/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
[ 21%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o
[ 21%] 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/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
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
[ 22%] 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
[ 22%] 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
[ 22%] 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
[ 22%] 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
[ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o
[ 22%] 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
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
[ 22%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o
[ 22%] 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/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
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
[ 23%] 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
[ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o
[ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_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/z_sin.c.o -MF CMakeFiles/vf2c.dir/z_sin.c.o.d -o CMakeFiles/vf2c.dir/z_sin.c.o -c /build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_sin.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/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
[ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_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/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
[ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o
[ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_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/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
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
[ 25%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o
[ 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
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
[ 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 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
[ 26%] 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
[ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_dim.c.o
[ 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
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
[ 27%] 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
[ 27%] 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
[ 28%] 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
[ 28%] 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
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
[ 28%] 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
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_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
[ 29%] Built target cgcode
[ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_mod.c.o
[ 29%] 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/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
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
[ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_nint.c.o
[ 29%] 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
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_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
[ 30%] 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
[ 30%] 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
[ 31%] 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
[ 31%] 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
[ 31%] 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
[ 31%] 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
[ 32%] 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
[ 32%] 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
[ 32%] 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
[ 32%] 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
[ 33%] 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
[ 33%] 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
[ 33%] 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
[ 34%] 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
[ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o
[ 34%] 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_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
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
[ 34%] 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 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
/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 *");
| ^~~~~~~~~
[ 35%] 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
/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");
| ^~~~~
[ 35%] 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
[ 35%] 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
[ 36%] 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
[ 36%] 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
[ 36%] 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
[ 36%] 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
[ 37%] 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
[ 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_indx.c.o
[ 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_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
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
[ 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
[ 41%] 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
[ 41%] 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
[ 41%] 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
[ 42%] 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
[ 42%] 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
[ 42%] 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
[ 43%] 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
[ 43%] 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
[ 43%] 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
[ 43%] 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
[ 44%] 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
[ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o
[ 44%] 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
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
[ 44%] 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
[ 45%] 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
[ 45%] 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
[ 45%] 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
[ 45%] 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
[ 46%] 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
[ 46%] 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
[ 46%] 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
[ 46%] 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
[ 47%] 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
[ 47%] 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
[ 47%] 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
[ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dtime_.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/dtime_.c.o -MF CMakeFiles/vf2c.dir/dtime_.c.o.d -o CMakeFiles/vf2c.dir/dtime_.c.o -c /build/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/dtime_.c
[ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/etime_.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/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
[ 48%] 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
/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 48%] 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
[ 49%] 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
/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);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 49%] 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
[ 49%] 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
[ 49%] 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
[ 49%] 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
[ 50%] 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
[ 50%] 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
[ 50%] 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
[ 50%] 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
[ 51%] 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
[ 52%] 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
[ 52%] 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
[ 52%] 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
[ 53%] 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
/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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");
| ^~~~~~~~
[ 53%] 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
[ 53%] 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
[ 53%] 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
[ 53%] 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
[ 53%] 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
[ 54%] 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 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
[ 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 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
[ 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
[ 56%] 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
[ 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
[ 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/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
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=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libvf2c.so.1.9 -o libvf2c.so.1.9.3 CMakeFiles/vf2c.dir/f77vers.c.o CMakeFiles/vf2c.dir/i77vers.c.o CMakeFiles/vf2c.dir/s_rnge.c.o CMakeFiles/vf2c.dir/abort_.c.o CMakeFiles/vf2c.dir/exit_.c.o CMakeFiles/vf2c.dir/getarg_.c.o CMakeFiles/vf2c.dir/iargc_.c.o CMakeFiles/vf2c.dir/getenv_.c.o CMakeFiles/vf2c.dir/signal_.c.o CMakeFiles/vf2c.dir/s_stop.c.o CMakeFiles/vf2c.dir/s_paus.c.o CMakeFiles/vf2c.dir/system_.c.o CMakeFiles/vf2c.dir/cabs.c.o CMakeFiles/vf2c.dir/derf_.c.o CMakeFiles/vf2c.dir/derfc_.c.o CMakeFiles/vf2c.dir/erf_.c.o CMakeFiles/vf2c.dir/erfc_.c.o CMakeFiles/vf2c.dir/sig_die.c.o CMakeFiles/vf2c.dir/uninit.c.o CMakeFiles/vf2c.dir/pow_ci.c.o CMakeFiles/vf2c.dir/pow_dd.c.o CMakeFiles/vf2c.dir/pow_di.c.o CMakeFiles/vf2c.dir/pow_hh.c.o CMakeFiles/vf2c.dir/pow_ii.c.o CMakeFiles/vf2c.dir/pow_ri.c.o CMakeFiles/vf2c.dir/pow_zi.c.o CMakeFiles/vf2c.dir/pow_zz.c.o CMakeFiles/vf2c.dir/c_abs.c.o CMakeFiles/vf2c.dir/c_cos.c.o CMakeFiles/vf2c.dir/c_div.c.o CMakeFiles/vf2c.dir/c_exp.c.o CMakeFiles/vf2c.dir/c_log.c.o CMakeFiles/vf2c.dir/c_sin.c.o CMakeFiles/vf2c.dir/c_sqrt.c.o CMakeFiles/vf2c.dir/z_abs.c.o CMakeFiles/vf2c.dir/z_cos.c.o CMakeFiles/vf2c.dir/z_div.c.o CMakeFiles/vf2c.dir/z_exp.c.o CMakeFiles/vf2c.dir/z_log.c.o CMakeFiles/vf2c.dir/z_sin.c.o CMakeFiles/vf2c.dir/z_sqrt.c.o CMakeFiles/vf2c.dir/r_abs.c.o CMakeFiles/vf2c.dir/r_acos.c.o CMakeFiles/vf2c.dir/r_asin.c.o CMakeFiles/vf2c.dir/r_atan.c.o CMakeFiles/vf2c.dir/r_atn2.c.o CMakeFiles/vf2c.dir/r_cnjg.c.o CMakeFiles/vf2c.dir/r_cos.c.o CMakeFiles/vf2c.dir/r_cosh.c.o CMakeFiles/vf2c.dir/r_dim.c.o CMakeFiles/vf2c.dir/r_exp.c.o CMakeFiles/vf2c.dir/r_imag.c.o CMakeFiles/vf2c.dir/r_int.c.o CMakeFiles/vf2c.dir/r_lg10.c.o CMakeFiles/vf2c.dir/r_log.c.o CMakeFiles/vf2c.dir/r_mod.c.o CMakeFiles/vf2c.dir/r_nint.c.o CMakeFiles/vf2c.dir/r_sign.c.o CMakeFiles/vf2c.dir/r_sin.c.o CMakeFiles/vf2c.dir/r_sinh.c.o CMakeFiles/vf2c.dir/r_sqrt.c.o CMakeFiles/vf2c.dir/r_tan.c.o CMakeFiles/vf2c.dir/r_tanh.c.o CMakeFiles/vf2c.dir/d_abs.c.o CMakeFiles/vf2c.dir/d_acos.c.o CMakeFiles/vf2c.dir/d_asin.c.o CMakeFiles/vf2c.dir/d_atan.c.o CMakeFiles/vf2c.dir/d_atn2.c.o CMakeFiles/vf2c.dir/d_cnjg.c.o CMakeFiles/vf2c.dir/d_cos.c.o CMakeFiles/vf2c.dir/d_cosh.c.o CMakeFiles/vf2c.dir/d_dim.c.o CMakeFiles/vf2c.dir/d_exp.c.o CMakeFiles/vf2c.dir/d_imag.c.o CMakeFiles/vf2c.dir/d_int.c.o CMakeFiles/vf2c.dir/d_lg10.c.o CMakeFiles/vf2c.dir/d_log.c.o CMakeFiles/vf2c.dir/d_mod.c.o CMakeFiles/vf2c.dir/d_nint.c.o CMakeFiles/vf2c.dir/d_prod.c.o CMakeFiles/vf2c.dir/d_sign.c.o CMakeFiles/vf2c.dir/d_sin.c.o CMakeFiles/vf2c.dir/d_sinh.c.o CMakeFiles/vf2c.dir/d_sqrt.c.o CMakeFiles/vf2c.dir/d_tan.c.o CMakeFiles/vf2c.dir/d_tanh.c.o CMakeFiles/vf2c.dir/i_abs.c.o CMakeFiles/vf2c.dir/i_dim.c.o CMakeFiles/vf2c.dir/i_dnnt.c.o CMakeFiles/vf2c.dir/i_indx.c.o CMakeFiles/vf2c.dir/i_len.c.o CMakeFiles/vf2c.dir/i_mod.c.o CMakeFiles/vf2c.dir/i_nint.c.o CMakeFiles/vf2c.dir/i_sign.c.o CMakeFiles/vf2c.dir/lbitbits.c.o CMakeFiles/vf2c.dir/lbitshft.c.o CMakeFiles/vf2c.dir/h_abs.c.o CMakeFiles/vf2c.dir/h_dim.c.o CMakeFiles/vf2c.dir/h_dnnt.c.o CMakeFiles/vf2c.dir/h_indx.c.o CMakeFiles/vf2c.dir/h_len.c.o CMakeFiles/vf2c.dir/h_mod.c.o CMakeFiles/vf2c.dir/h_nint.c.o CMakeFiles/vf2c.dir/h_sign.c.o CMakeFiles/vf2c.dir/l_ge.c.o CMakeFiles/vf2c.dir/l_gt.c.o CMakeFiles/vf2c.dir/l_le.c.o CMakeFiles/vf2c.dir/l_lt.c.o CMakeFiles/vf2c.dir/hl_ge.c.o CMakeFiles/vf2c.dir/hl_gt.c.o CMakeFiles/vf2c.dir/hl_le.c.o CMakeFiles/vf2c.dir/hl_lt.c.o CMakeFiles/vf2c.dir/ef1asc_.c.o CMakeFiles/vf2c.dir/ef1cmc_.c.o CMakeFiles/vf2c.dir/f77_aloc.c.o CMakeFiles/vf2c.dir/s_cat.c.o CMakeFiles/vf2c.dir/s_cmp.c.o CMakeFiles/vf2c.dir/s_copy.c.o CMakeFiles/vf2c.dir/dtime_.c.o CMakeFiles/vf2c.dir/etime_.c.o CMakeFiles/vf2c.dir/backspac.c.o CMakeFiles/vf2c.dir/close.c.o CMakeFiles/vf2c.dir/dfe.c.o CMakeFiles/vf2c.dir/dolio.c.o CMakeFiles/vf2c.dir/due.c.o CMakeFiles/vf2c.dir/endfile.c.o CMakeFiles/vf2c.dir/err.c.o CMakeFiles/vf2c.dir/fmt.c.o CMakeFiles/vf2c.dir/fmtlib.c.o CMakeFiles/vf2c.dir/ftell_.c.o CMakeFiles/vf2c.dir/iio.c.o CMakeFiles/vf2c.dir/ilnw.c.o CMakeFiles/vf2c.dir/inquire.c.o CMakeFiles/vf2c.dir/lread.c.o CMakeFiles/vf2c.dir/lwrite.c.o CMakeFiles/vf2c.dir/open.c.o CMakeFiles/vf2c.dir/rdfmt.c.o CMakeFiles/vf2c.dir/rewind.c.o CMakeFiles/vf2c.dir/rsfe.c.o CMakeFiles/vf2c.dir/rsli.c.o CMakeFiles/vf2c.dir/rsne.c.o CMakeFiles/vf2c.dir/sfe.c.o CMakeFiles/vf2c.dir/sue.c.o CMakeFiles/vf2c.dir/typesize.c.o CMakeFiles/vf2c.dir/uio.c.o CMakeFiles/vf2c.dir/util.c.o CMakeFiles/vf2c.dir/wref.c.o CMakeFiles/vf2c.dir/wrtfmt.c.o CMakeFiles/vf2c.dir/wsfe.c.o CMakeFiles/vf2c.dir/wsle.c.o CMakeFiles/vf2c.dir/wsne.c.o CMakeFiles/vf2c.dir/xwsne.c.o CMakeFiles/vf2c.dir/main.c.o
cd /build/apbs-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 _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build
make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[ 60%] Building C object _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o
cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cc -Dpunc_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 -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/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 directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/base/mc_base.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
[ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bmat.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/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/bam/bvec.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/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
[ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o
[ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matcopy.c.o
[ 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/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
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
[ 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
/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/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/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/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 ());
| ~~~~~~~~~~~~~~~~~
/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 ());
| ~~~~~~~~~~~~~~~~~
[ 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
[ 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
[ 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/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/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/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
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
[ 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
[ 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
/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 ());
| ~~~~~~~~~~~~~~~~~
[ 66%] 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
/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 ());
| ~~~~~~~~~~~~~~~~~
[ 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
/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 ());
| ~~~~~~~~~~~~~~~~~
[ 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 ());
| ~~~~~~~~~~~~~~~~~
/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 ());
| ~~~~~~~~~~~~~~~~~
[ 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
[ 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
[ 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/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/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
/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,
| ^~~~~~~~~~~
[ 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
/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/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
[ 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/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/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: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 -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.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/generic /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic/CMakeFiles/apbs_generic.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/src/pmgc /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc /build/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc/CMakeFiles/apbs_pmgc.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/build
make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
make[3]: Leaving 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/build
make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o
[ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.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/nosh.c.o -MF CMakeFiles/apbs_generic.dir/nosh.c.o.d -o CMakeFiles/apbs_generic.dir/nosh.c.o -c /build/apbs-3.4.1/src/generic/nosh.c
[ 75%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o
[ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.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/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
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/buildAd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildAd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildAd.c.o -c /build/apbs-3.4.1/src/pmgc/buildAd.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 -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/mgparm.c.o -MF CMakeFiles/apbs_generic.dir/mgparm.c.o.d -o CMakeFiles/apbs_generic.dir/mgparm.c.o -c /build/apbs-3.4.1/src/generic/mgparm.c
[ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.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
[ 75%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.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/buildBd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildBd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildBd.c.o -c /build/apbs-3.4.1/src/pmgc/buildBd.c
[ 76%] 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/pbsamparm.c.o -MF CMakeFiles/apbs_generic.dir/pbsamparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbsamparm.c.o -c /build/apbs-3.4.1/src/generic/pbsamparm.c
[ 76%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.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/pbeparm.c.o -MF CMakeFiles/apbs_generic.dir/pbeparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbeparm.c.o -c /build/apbs-3.4.1/src/generic/pbeparm.c
[ 76%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.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/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 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildPd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildPd.c.o -c /build/apbs-3.4.1/src/pmgc/buildPd.c
[ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.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/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 -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/vpbe.c.o -MF CMakeFiles/apbs_generic.dir/vpbe.c.o.d -o CMakeFiles/apbs_generic.dir/vpbe.c.o -c /build/apbs-3.4.1/src/generic/vpbe.c
[ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.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/vcap.c.o -MF CMakeFiles/apbs_generic.dir/vcap.c.o.d -o CMakeFiles/apbs_generic.dir/vcap.c.o -c /build/apbs-3.4.1/src/generic/vcap.c
[ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.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/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 src/generic/CMakeFiles/apbs_generic.dir/vstring.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/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 -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/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
[ 81%] 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
[ 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/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
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'
[ 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%] 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'
[ 83%] 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
[ 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
[ 83%] 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
[ 84%] 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
[ 84%] 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
[ 84%] 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
[ 84%] 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/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
[ 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 '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;
| ^
/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/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
[ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o
[ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o
[ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o
[ 87%] 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/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
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
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
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
/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
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
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
/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,
| ^~~~~~~~~~~~~~~~~~
[ 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
/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
/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 ());
| ~~~~~~~~~~~~~~~~~
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 '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 -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.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[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/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/depend
make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/depend
make[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 /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/dxmath.dir/DependInfo.cmake --color=
make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.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/mergedx.dir/DependInfo.cmake --color=
make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.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/mergedx2.dir/DependInfo.cmake --color=
make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.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/value.dir/DependInfo.cmake --color=
make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/depend
make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
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/multivalue.dir/DependInfo.cmake --color=
make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.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'
make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/build
make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.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'
make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/build
make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/build
[ 89%] Building C object tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o
make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/build
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/mgmesh.dir/mgmesh.c.o -MF CMakeFiles/mgmesh.dir/mgmesh.c.o.d -o CMakeFiles/mgmesh.dir/mgmesh.c.o -c /build/apbs-3.4.1/tools/mesh/mgmesh.c
make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[ 89%] Building C object tools/mesh/CMakeFiles/smooth.dir/smooth.c.o
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/value.dir/build.make tools/mesh/CMakeFiles/value.dir/build
[ 89%] Building C object tools/mesh/CMakeFiles/dxmath.dir/dxmath.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/smooth.dir/smooth.c.o -MF CMakeFiles/smooth.dir/smooth.c.o.d -o CMakeFiles/smooth.dir/smooth.c.o -c /build/apbs-3.4.1/tools/mesh/smooth.c
[ 90%] Building C object tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o
make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/build
make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
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/dxmath.dir/dxmath.c.o -MF CMakeFiles/dxmath.dir/dxmath.c.o.d -o CMakeFiles/dxmath.dir/dxmath.c.o -c /build/apbs-3.4.1/tools/mesh/dxmath.c
make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[ 90%] Building C object src/CMakeFiles/apbs.dir/main.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/mergedx.dir/mergedx.c.o -MF CMakeFiles/mergedx.dir/mergedx.c.o.d -o CMakeFiles/mergedx.dir/mergedx.c.o -c /build/apbs-3.4.1/tools/mesh/mergedx.c
[ 90%] Building C object tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o
cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src && /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 -fPIE -fopenmp -MD -MT src/CMakeFiles/apbs.dir/main.c.o -MF CMakeFiles/apbs.dir/main.c.o.d -o CMakeFiles/apbs.dir/main.c.o -c /build/apbs-3.4.1/src/main.c
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/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
[ 91%] Building C object tools/mesh/CMakeFiles/multivalue.dir/multivalue.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/multivalue.dir/multivalue.c.o -MF CMakeFiles/multivalue.dir/multivalue.c.o.d -o CMakeFiles/multivalue.dir/multivalue.c.o -c /build/apbs-3.4.1/tools/mesh/multivalue.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
[ 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/mgmesh.dir/link.txt --verbose=1
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/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
/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
/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
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'
[ 92%] Built target value
[ 92%] Built target mgmesh
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 -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.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/similarity.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'
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'
[ 92%] Building C object tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o
[ 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 -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/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
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/similarity.dir/similarity.c.o -MF CMakeFiles/similarity.dir/similarity.c.o.d -o CMakeFiles/similarity.dir/similarity.c.o -c /build/apbs-3.4.1/tools/mesh/similarity.c
make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[ 92%] Built target multivalue
make -f tools/mesh/CMakeFiles/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.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/analysis.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/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.dir/build
make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[ 92%] Built target smooth
[ 92%] Linking C executable apbs
make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/depend
cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs.dir/link.txt --verbose=1
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/dx2mol.dir/DependInfo.cmake --color=
[ 92%] Building C object tools/mesh/CMakeFiles/analysis.dir/analysis.c.o
/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/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
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/analysis.dir/analysis.c.o -MF CMakeFiles/analysis.dir/analysis.c.o.d -o CMakeFiles/analysis.dir/analysis.c.o -c /build/apbs-3.4.1/tools/mesh/analysis.c
make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.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/dx2mol.dir/dx2mol.c.o
[ 92%] Built target dxmath
make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/depend
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/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]: 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/dx2uhbd.dir/DependInfo.cmake --color=
[ 92%] Linking C executable ../bin/mergedx
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
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
make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[ 92%] Building C object tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o
/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
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
[ 92%] 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'
[ 92%] Built target apbs
make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.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/del2dx.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[ 93%] Linking C executable ../bin/benchmark
make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/build
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
make[3]: Entering 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/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
make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[ 93%] Linking C executable ../bin/dx2mol
[ 93%] Building C object tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o
cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2mol.dir/link.txt --verbose=1
[ 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 CMakeFiles/dx2uhbd.dir/link.txt --verbose=1
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/del2dx.dir/del2dx.c.o -MF CMakeFiles/del2dx.dir/del2dx.c.o.d -o CMakeFiles/del2dx.dir/del2dx.c.o -c /build/apbs-3.4.1/tools/mesh/del2dx.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/dx2uhbd.dir/dx2uhbd.c.o -o ../bin/dx2uhbd ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/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
[ 94%] Built target mergedx
make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.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/tensor2dx.dir/DependInfo.cmake --color=
/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/dx2mol.dir/dx2mol.c.o -o ../bin/dx2mol ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/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 -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/build
make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[ 95%] Building C object tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o
make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
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/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
[ 96%] Linking C executable ../bin/analysis
cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysis.dir/link.txt --verbose=1
[ 96%] Built target mergedx2
/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 -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.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/uhbd_asc2bin.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build
make[3]: Entering directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[ 96%] Building C object tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.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/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -MF CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o.d -o CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -c /build/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c
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'
/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 96%] Built target benchmark
[ 97%] Linking C executable ../bin/similarity
[ 97%] Built target dx2uhbd
make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/depend
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
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/coulomb.dir/DependInfo.cmake --color=
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=
/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/similarity.dir/similarity.c.o -o ../bin/similarity ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/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 -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.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'
make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.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'
[ 97%] Building C object tools/manip/CMakeFiles/born.dir/born.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/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
[ 97%] Built target dx2mol
make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.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/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.dir/DependInfo.cmake --color=
[ 98%] 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
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/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/build
/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/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);
| ^~~~~~~~~~~~~~~~~
[ 98%] Built target analysis
/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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Entering 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/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/python-pybind /build/apbs-3.4.1/obj-aarch64-linux-gnu /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind/CMakeFiles/apbs_pybind.dir/DependInfo.cmake --color=
[ 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
[ 99%] Building C object tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o
/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
cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python && /usr/bin/cc -D_apbslib_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/python3.11 -I/build/apbs-3.4.1/tools/python -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 tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -MF CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o.d -o CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -c /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.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'
[ 99%] 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
[ 99%] Linking C executable ../bin/tensor2dx
cd /build/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/tensor2dx.dir/link.txt --verbose=1
[ 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
/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/tensor2dx.dir/tensor2dx.c.o -o ../bin/tensor2dx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/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/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
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 del2dx
[100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o
[100%] Linking C executable ../bin/born
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
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
/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%] 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/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'
[100%] Built target uhbd_asc2bin
make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[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
[100%] Built target tensor2dx
make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[100%] Built target born
make[3]: Leaving directory '/build/apbs-3.4.1/obj-aarch64-linux-gnu'
[100%] Built target coulomb
[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.read.
Possible hints:
* ModuleNotFoundError: No module named 'pyparsing'
* AttributeError: module 'apbs' has no attribute 'input_file'
Failed to import apbs.input_file.calculate.boundary_element.
Possible hints:
* ModuleNotFoundError: No module named 'pyparsing'
* AttributeError: module 'apbs' has no attribute 'input_file'
Failed to import apbs.input_file.calculate.nonpolar.Nonpolar.
Possible hints:
* ModuleNotFoundError: No module named 'pyparsing'
* AttributeError: module 'apbs' has no attribute 'input_file'
Failed to import apbs.input_file.
Possible hints:
* ModuleNotFoundError: No module named 'pyparsing'
* AttributeError: module 'apbs' has no attribute 'input_file'
Failed to import apbs.input_file.process.
Possible hints:
* ModuleNotFoundError: No module named 'pyparsing'
* AttributeError: module 'apbs' has no attribute 'input_file'
Failed to import apbs.input_file.calculate.
Possible hints:
* ModuleNotFoundError: No module named 'pyparsing'
* AttributeError: module 'apbs' has no attribute 'input_file'
Failed to import apbs.input_file.calculate.generic.
Possible hints:
* ModuleNotFoundError: No module named 'pyparsing'
* AttributeError: module 'apbs' has no attribute 'input_file'
Failed to import apbs.input_file.calculate.finite_difference.
Possible hints:
* ModuleNotFoundError: No module named 'pyparsing'
* AttributeError: module 'apbs' has no attribute 'input_file'
Failed to import apbs.input_file.calculate.finite_element.
Possible hints:
* ModuleNotFoundError: No module named 'pyparsing'
* AttributeError: module 'apbs' has no attribute 'input_file'
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 <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff7fa20550>: 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... [ 21%] using/input/new/calculate/boundary_element
writing output... [ 22%] using/input/new/calculate/finite_difference
writing output... [ 22%] using/input/new/calculate/finite_element
writing output... [ 23%] using/input/new/calculate/index
writing output... [ 24%] using/input/new/calculate/nonpolar
writing output... [ 25%] using/input/new/index
writing output... [ 25%] using/input/new/process
writing output... [ 26%] using/input/new/process_api
writing output... [ 27%] using/input/new/read
writing output... [ 28%] using/input/old/apolar/dpos
writing output... [ 29%] using/input/old/apolar/gamma
writing output... [ 29%] using/input/old/apolar/index
writing output... [ 30%] using/input/old/apolar/press
writing output... [ 31%] using/input/old/apolar/srfm
writing output... [ 32%] using/input/old/elec/3dmap
writing output... [ 33%] using/input/old/elec/akeyPRE
writing output... [ 33%] using/input/old/elec/akeySOLVE
writing output... [ 34%] using/input/old/elec/async
writing output... [ 35%] using/input/old/elec/bcfl
writing output... [ 36%] using/input/old/elec/cgcent
writing output... [ 37%] using/input/old/elec/cglen
writing output... [ 37%] using/input/old/elec/chgm
writing output... [ 38%] using/input/old/elec/diff
writing output... [ 39%] using/input/old/elec/dime
writing output... [ 40%] using/input/old/elec/domainLength
writing output... [ 40%] using/input/old/elec/dx
writing output... [ 41%] using/input/old/elec/ekey
writing output... [ 42%] using/input/old/elec/etol
writing output... [ 43%] using/input/old/elec/exp
writing output... [ 44%] using/input/old/elec/fe-manual
writing output... [ 44%] using/input/old/elec/fgcent
writing output... [ 45%] using/input/old/elec/fglen
writing output... [ 46%] using/input/old/elec/gamma-geoflow
writing output... [ 47%] using/input/old/elec/gcent
writing output... [ 48%] using/input/old/elec/geoflow-auto
writing output... [ 48%] using/input/old/elec/glen
writing output... [ 49%] using/input/old/elec/grid2d
writing output... [ 50%] using/input/old/elec/gridpts
writing output... [ 51%] using/input/old/elec/imat
writing output... [ 51%] using/input/old/elec/index
writing output... [ 52%] using/input/old/elec/ion
writing output... [ 53%] using/input/old/elec/lpbe
writing output... [ 54%] using/input/old/elec/lrpbe
writing output... [ 55%] using/input/old/elec/mac
writing output... [ 55%] using/input/old/elec/maxsolve
writing output... [ 56%] using/input/old/elec/maxvert
writing output... [ 57%] using/input/old/elec/mesh
writing output... [ 58%] using/input/old/elec/mg-auto
writing output... [ 59%] using/input/old/elec/mg-dummy
writing output... [ 59%] using/input/old/elec/mg-manual
writing output... [ 60%] using/input/old/elec/mg-para
writing output... [ 61%] using/input/old/elec/nlev
writing output... [ 62%] using/input/old/elec/npbe
writing output... [ 62%] using/input/old/elec/nrpbe
writing output... [ 63%] using/input/old/elec/ntraj
writing output... [ 64%] using/input/old/elec/ofrac
writing output... [ 65%] using/input/old/elec/outdata
writing output... [ 66%] using/input/old/elec/pbam-auto
writing output... [ 66%] using/input/old/elec/pbc
writing output... [ 67%] using/input/old/elec/pbsam-auto
writing output... [ 68%] using/input/old/elec/pdie
writing output... [ 69%] using/input/old/elec/pdime
writing output... [ 70%] using/input/old/elec/press-geoflow
writing output... [ 70%] using/input/old/elec/pygbe
writing output... [ 71%] using/input/old/elec/randorient
writing output... [ 72%] using/input/old/elec/runname
writing output... [ 73%] using/input/old/elec/runtype
writing output... [ 74%] using/input/old/elec/salt
writing output... [ 74%] using/input/old/elec/sdie
writing output... [ 75%] using/input/old/elec/srfm
writing output... [ 76%] using/input/old/elec/surf
writing output... [ 77%] using/input/old/elec/tabi
writing output... [ 77%] using/input/old/elec/targetNum
writing output... [ 78%] using/input/old/elec/targetRes
writing output... [ 79%] using/input/old/elec/term
writing output... [ 80%] using/input/old/elec/termcombine
writing output... [ 81%] using/input/old/elec/tolsp
writing output... [ 81%] using/input/old/elec/tree_n0
writing output... [ 82%] using/input/old/elec/tree_order
writing output... [ 83%] using/input/old/elec/units
writing output... [ 84%] using/input/old/elec/usemap
writing output... [ 85%] using/input/old/elec/usemesh
writing output... [ 85%] using/input/old/elec/vdwdisp
writing output... [ 86%] using/input/old/elec/write
writing output... [ 87%] using/input/old/elec/writemat
writing output... [ 88%] using/input/old/elec/xyz
writing output... [ 88%] using/input/old/generic/bconc
writing output... [ 89%] using/input/old/generic/calcenergy
writing output... [ 90%] using/input/old/generic/calcforce
writing output... [ 91%] using/input/old/generic/grid
writing output... [ 92%] using/input/old/generic/mol
writing output... [ 92%] using/input/old/generic/sdens
writing output... [ 93%] using/input/old/generic/srad
writing output... [ 94%] using/input/old/generic/swin
writing output... [ 95%] using/input/old/generic/temp
writing output... [ 96%] using/input/old/index
writing output... [ 96%] using/input/old/print
writing output... [ 97%] using/input/old/read
writing output... [ 98%] using/tests
writing output... [ 99%] using/tools
writing output... [100%] using/units
generating indices... genindex py-modindex done
writing additional pages... search done
copying images... [ 10%] media/pb-schematic.png
copying images... [ 20%] media/apbs_bind_eng.png
copying images... [ 30%] media/rna-qdens-pymol.jpg
copying images... [ 40%] media/rna-qdens-vmd.jpg
copying images... [ 50%] media/apbs_sol_eng.png
copying images... [ 60%] media/fas2-iso-pymol.png
copying images... [ 70%] media/fas2-surf-pymol.png
copying images... [ 80%] media/1fas_VR.png
copying images... [ 90%] media/UI.png
copying images... [100%] media/AChE.png
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 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: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libpunc.so.1.9
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libpunc.so
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/punc/varpack.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/punc/vblas.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/punc/vcgcode.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/punc/vlapack.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/punc/vpmg.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/punc/vf2c.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libvf2c.so
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libcgcode.so
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/gamer/gamer.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/gamer/gamer_base.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/gamer/triangle.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/gamer/tetgen.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/gamer/biom.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgamer.so.1.9.3
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgamer.so.1.9
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgamer.so
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/mc_base.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/mc.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/bam.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/bmat.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/bvec.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/mat.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/mtool.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/slu.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/vec.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/vec3.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/zslu.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/whb.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/aprx.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/bnode.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/node.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/re.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/gem.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/vel.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/ves.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/pde.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/am.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/nam.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/dyn.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mc/mcsh.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libmc.so.1.9.3
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libmc.so.1.9
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libmc.so
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_routines.so.3
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_routines.so
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/apbs/apbs.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/apbs/routines.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/bin/apbs
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/nosh.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/mgparm.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/femparm.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/pbamparm.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/pbsamparm.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/pbeparm.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/bemparm.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/geoflowparm.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/apolparm.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/vacc.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/valist.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/vatom.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/vpbe.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/vcap.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/vclist.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/vstring.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/vparam.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/vgreen.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/vmatrix.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/vhal.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/generic/vunit.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_generic.so.3
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_generic.so
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/buildAd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/buildBd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/buildGd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/buildPd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/cgd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/gsd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/matvecd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/mgcsd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/mgdrvd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/mgsubd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/mikpckd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/mlinpckd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/mypdec.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/newtond.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/newdrvd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/powerd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/smoothd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/pmgc/mgfasd.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_pmgc.so.3
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_pmgc.so
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mg/vgrid.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mg/vmgrid.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mg/vopot.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mg/vpmg.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/mg/vpmgp.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_mg.so.3
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_mg.so
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/fem/vcsm.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/fem/vfetk.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/include/fem/vpee.h
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_fem.so.3
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_fem.so
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/lib/apbs.cpython-311-aarch64-linux-gnu.so
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/methoxide.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/methanol.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/apbs-smol.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/apbs-mol.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/UHBD
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.out.orig.exam
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.inp.exam
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.dat.exam
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/solv/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/run_selected_examples.sh
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/run_examples.sh
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys1_charges.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys.param
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys.config
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_stern.vert
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_stern.face
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_3.vert
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_3.face
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_2.vert
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_2.face
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_1.vert
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_1.face
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1.vert
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1.face
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pygbe/lys.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/postprocess.sh
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/apbs_dx.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/fit.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/test.sh
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/template.txt
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/run_apdx_files.sh
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/model_outNpep.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/model_outNB.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/model_outBoxB19.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath.txt
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/PDB
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outNpep.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outNB.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outBoxB19.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/runme.sh
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/point-pmf-0.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/mol4.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/mol3.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/mol2.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/mol1.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/mol0.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/energy.dat
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_4.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_4.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_3.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_3.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_2.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_2.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_1.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_1.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/apbs.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/point-pmf/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_lig_apbs.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_bin_apbs.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_apo_apbs.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-vdw.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-surf.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-vdw.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-surf.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-lig.out
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-bin.out
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-apo.out
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-lig.out
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-bin.out
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-apo.out
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/README
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pka-lig/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_2_2.xyz
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_2_1.xyz
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_1_2.xyz
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_1_1.xyz
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_msms.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_electrostatic.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_energyforce.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_electrostatic.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_dynamics.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg2.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.vert
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-gly/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barstar.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barnase.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barn_bars_electro.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/toy_energyforce.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/toy_electrostatic.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/toy_dynamics.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/pos_charge.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/pos_3.xyz
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/pos_2.xyz
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/pos_1.xyz
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/neg_charge.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/neg_3.xyz
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/neg_2.xyz
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/neg_1.xyz
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/1a63.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/pbam/1a63.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc/param.dat
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc/mache.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc/fas2.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc/apbs.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc/apbs-PDB.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc/achbp.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/misc/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/proton.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/apbs-smol.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/apbs-mol.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/acetic-acid.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/acetate.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/UHBD
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.pdb.exam
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.out.orig.exam
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.inp.exam
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.dat.exam
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ionize/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/small491.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/complex.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel2.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel12.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel2.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel12.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.log
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.inp
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.e2.log
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/491.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-protein/491.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/runme.sh
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/polarforces
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/parm.dat
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/complex.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/apolarforces
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/draw_membrane2.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Run_membrane-helix.sh
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-8.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-4.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-16.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-12.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-0.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Apbs_solv-TEMPLATE.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy-TEMPLATE.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/mesh.m
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/hca.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/complex.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-smol.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-mol.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/acet.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/srsrf.dot
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.qcd
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.err
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf1.qcd
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf.log
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf.inp
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.out
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.inp
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.err
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/imidazole_zap.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/imidazole.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/glycerol.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/gly.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/gly.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/1a63.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/geoflow/1a63.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/polarforces
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/pmf.dat
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/parm.dat
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/mesh.m
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/ion.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apolarforces
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-smol-parallel.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-smol-fem.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-smol-auto.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-mol-parallel.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-mol-fem.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-mol-fem-extmesh.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-mol-auto.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-forces.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/apbs-apolar.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/born/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins/twob2.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins/twob.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins/oneb.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins/451c.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1bbl.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1ajj.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1a63.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/451c_order5.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/451c_order1.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/1a63_NanoShaper_Skin.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem/1a63_NanoShaper_SES.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/ASP66.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/ASH66.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASP66.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASH66.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASP66.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASH66.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/ASP66.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/ASH66.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-noASP66.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-noASH66.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASP66.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASH66.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer2.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer1.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30_monomer2.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30_monomer1.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/propane.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/pentane.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/parm.dat
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/neopentane.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/mol.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/methane.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/isobutane.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/hexane.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/force.result
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/ethane.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/cyclopentane.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/cyclohexane.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/butane.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/apbs-forces.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/alkanes.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/2-methylbutane.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/mol2.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/mol1.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/mesh.m
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/complex.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-auto.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-auto.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/srsrf.dot
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/single.inp
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/prot4.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/prot3.pdb
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.inp
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.full.log
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/aheall-atom.charmm.dat
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/actin-dimer/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/dss-min.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/dmso-min.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-min.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/dss-min.qcd
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.log
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.inp
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/1d7i-min.qcd
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-smol.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-mol.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-complex.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-min.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/pqr2qcd
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/dmso-min.qcd
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.oldlog
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.log
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.inp
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/1d7h-min.qcd
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-smol.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-mol.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-complex.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tests
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tests/test_cases.cfg
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tests/apbs_tester.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tests/apbs_check_intermediate_energies.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tests/apbs_check_results.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tests/apbs_check_forces.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tests/apbs_logger.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tests/README.md
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.net
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.cfg
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.net
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cm
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cfg
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.net
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cm
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cfg
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.net
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.cfg
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/CMakeLists.txt
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/noinput.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/vgridlib.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/vgrid.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/vgrid.i
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/read.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/mergedx.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/average.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/README
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile.am
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/main.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/ion.pqr
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/apbslib_wrap.doc
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/apbslib.i
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/apbslib.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/apbs.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/README
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/Makefile.in
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/Makefile.am
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python/Makefile
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/module.cpp
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_vatom.hpp
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_vatom.cpp
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_valist.hpp
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_valist.cpp
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_nosh.hpp
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_nosh.cpp
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_constants.hpp
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/CMakeLists.txt
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/value.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/uhbd_asc2bin.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/tensor2dx.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/smooth.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/similarity.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/multivalue.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/mgmesh.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/mergedx2.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/mergedx.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/dxmath.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/dx2uhbd.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/dx2mol.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/del2dx.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/benchmark.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/analysis.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/mesh/CMakeLists.txt
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip/inputgen.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip/psize.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip/coulomb.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip/born.c
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip/CMakeLists.txt
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/github
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/github/release-data.py
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/github/getReleases.sh
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion
-- Installing: /build/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/qcd2pqr.awk
-- Installing: /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/coulomb
-- 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/uhbd_asc2bin
-- 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/del2dx
-- 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/benchmark
-- 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/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: 0.004454 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 14.678589 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 12.406689 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 63.705548 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 63.087297 seconds
--------------------------------------------------------------------------------
Total elapsed time: 153.882577 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 536.963669 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 368.255996 seconds
--------------------------------------------------------------------------------
Total elapsed time: 905.219665 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 45.196099 seconds
--------------------------------------------------------------------------------
Total elapsed time: 45.196099 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 65.48821 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 54.329274 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 63.784311 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 51.935225 seconds
--------------------------------------------------------------------------------
Total elapsed time: 235.53702 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 63.428965 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 50.083528 seconds
--------------------------------------------------------------------------------
Total elapsed time: 113.512493 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 34.763714 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 28.238283 seconds
--------------------------------------------------------------------------------
Total elapsed time: 63.001997 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 30.514371 seconds
--------------------------------------------------------------------------------
Total elapsed time: 30.514371 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 87.791857 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 60.426063 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 64.631278 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 54.551911 seconds
--------------------------------------------------------------------------------
Total elapsed time: 267.401109 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 6.925186 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 7.242716 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 6.699576 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 6.458477 seconds
--------------------------------------------------------------------------------
Total elapsed time: 27.325955 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 9.360711 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> 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: 8.591544 seconds
--------------------------------------------------------------------------------
Total elapsed time: 17.952255 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 saxpy_ 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 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 do_fio 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 sqrtf 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 e_wsfe 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 daxpy_ 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: 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 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 erf 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 exp 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 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 sqrt 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 cosh 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 tan 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: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx were not linked against libmc.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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx 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/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/multivalue 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/value debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx were not linked against libvf2c.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 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: 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 '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 'libapbs3-dbgsym' in '../libapbs3-dbgsym_3.4.1-5_arm64.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: 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/17545 and its subdirectories
I: Current time: Sun Apr 16 07:12:24 -12 2023
I: pbuilder-time-stamp: 1681672344